diff --git a/.dockerignore b/.dockerignore index a637a6b..911ae83 100644 --- a/.dockerignore +++ b/.dockerignore @@ -2,5 +2,6 @@ /examples/ /images/ /git-hooks/ -/*.* +/CHANGES.md +/README.md /LICENSE diff --git a/.travis.yml b/.travis.yml index bdfef3d..0a6dc01 100644 --- a/.travis.yml +++ b/.travis.yml @@ -44,4 +44,3 @@ script: - docker run -t --rm dockstore-cgpwgs alleleCounter --version - docker run -t --rm dockstore-cgpwgs brass.pl -version - docker run -t --rm dockstore-cgpwgs ascat.pl -version - - docker run -t --rm dockstore-cgpwgs battenberg.pl -version diff --git a/CHANGES.md b/CHANGES.md index 8b05309..3ae3015 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,5 +1,25 @@ # CHANGES +## 2.1.0 + +* Update base image to dockstore-cgpwxs:3.1.6 (from 3.0.3) + * Includes, memory footprint reduction for Caveman flagging + * Significant speedup in inde input generation + * Parallel flagging for SNV + * Fragment based SNV/Indel calling +* Upgrade allele counter and brass +* Reduce number of layers in final image. +* Remove some legacy env vars from wrappers +* Battenberg removed + * Was only included to do base allele counts not complete analysis + * Underlying data files are not supported for new builds or other species + * Contact [original authors](https://github.com/Wedge-Oxford/battenberg) for ongoing support +* Wrapper script didn't explicitly specify sex SNP loci file (ASCAT) + * no impact for GRCh37 other species/build would have used wrong sex chromosome SNPs +* CaVEMan step wasn't being passed normal contamination value, scientific impact: + * previously `caveman.pl` default of `0.1` was applied + * this will now honor the value from ASCAT (`1-$rho`) + ## 2.0.2 * Correct skipqc flag diff --git a/Dockerfile b/Dockerfile index 3637e58..841d807 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM quay.io/wtsicgp/dockstore-cgpwxs:3.0.3 as builder +FROM quay.io/wtsicgp/dockstore-cgpwxs:3.1.6 as builder USER root @@ -58,39 +58,42 @@ MAINTAINER keiranmraine@gmail.com LABEL vendor="Cancer Genome Project, Wellcome Trust Sanger Institute" LABEL uk.ac.sanger.cgp.description="CGP WGS pipeline for dockstore.org" -LABEL uk.ac.sanger.cgp.version="2.0.2" - -RUN bash -c 'apt-get update -yq >& this.log || (cat this.log 1>&2 && exit 1)' -RUN bash -c 'apt-get install -qy --no-install-recommends lsb-release >& this.log || (cat this.log 1>&2 && exit 1)' - -RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`/" >> /etc/apt/sources.list -RUN gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 -RUN gpg -a --export E084DAB9 | apt-key add - - -RUN bash -c 'apt-get update -yq >& this.log || (cat this.log 1>&2 && exit 1)' -RUN bash -c 'apt-get install -yq --no-install-recommends\ - apt-transport-https\ - locales\ - curl\ - ca-certificates\ - libperlio-gzip-perl\ - libssh2-1\ - bzip2\ - psmisc\ - time\ - zlib1g\ - liblzma5\ - libncurses5\ - libcairo2\ - gfortran\ - r-base\ - exonerate\ - libboost-iostreams-dev\ - p11-kit\ - >& this.log || (cat this.log 1>&2 && exit 1)' - -RUN bash -c 'locale-gen en_US.UTF-8 >& this.log || (cat this.log 1>&2 && exit 1)' -RUN bash -c 'update-locale LANG=en_US.UTF-8 >& this.log || (cat this.log 1>&2 && exit 1)' +LABEL uk.ac.sanger.cgp.version="2.1.0" + +RUN apt-get update -yq && \ +apt-get install -qy --no-install-recommends lsb-release + +RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`/" >> /etc/apt/sources.list && \ +gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 && \ +gpg -a --export E084DAB9 | apt-key add - + +RUN apt-get update -yq && \ +apt-get install -yq --no-install-recommends \ +apt-transport-https \ +locales \ +curl \ +ca-certificates \ +libperlio-gzip-perl \ +libssh2-1 \ +bzip2 \ +psmisc \ +time \ +zlib1g \ +liblzma5 \ +libncurses5 \ +libcairo2 \ +gfortran \ +r-base \ +exonerate \ +libboost-iostreams-dev \ +p11-kit \ +unattended-upgrades && \ +unattended-upgrade -d -v && \ +apt-get remove -yq unattended-upgrades && \ +apt-get autoremove -yq + +RUN locale-gen en_US.UTF-8 && \ +update-locale LANG=en_US.UTF-8 ENV OPT /opt/wtsi-cgp ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH diff --git a/README.md b/README.md index 6f1c7a4..e838fc9 100644 --- a/README.md +++ b/README.md @@ -12,21 +12,17 @@ the [Dockstore.org](https://dockstore.org/) framework. | --------------------------------------------- | ----------------------------------------------- | | [![Master Badge][travis-master]][travis-base] | [![Develop Badge][travis-develop]][travis-base] | - - -- [Usage](#usage) - - [Usable Cores](#usable-cores) -- [Other uses](#other-uses) - - [Native docker](#native-docker) - - [Singularity](#singularity) -- [Verifying your deployment](#verifying-your-deployment) -- [Example data](#example-data) -- [Diagram of internals](#diagram-of-internals) -- [Development environment](#development-environment) -- [Release process](#release-process) -- [LICENCE](#licence) - - +* [Usage](#usage) + * [Usable Cores](#usable-cores) +* [Other uses](#other-uses) + * [Native docker](#native-docker) + * [Singularity](#singularity) +* [Verifying your deployment](#verifying-your-deployment) +* [Example data](#example-data) +* [Diagram of internals](#diagram-of-internals) +* [Development environment](#development-environment) +* [Release process](#release-process) +* [LICENCE](#licence) ## Usage @@ -40,14 +36,14 @@ You should see the usage for the `ds-cgpwgs.pl` script for all parameters (or th Required input files are 1. Tumour BAM file -1. Normal BAM file -1. Core reference archive (e.g. [core_ref_GRCh37d5.tar.gz][ftp-ref]) -1. WXS reference archive (e.g. [SNV_INDEL_ref_GRCh37d5.tar.gz][ftp-ref]) -1. WGS reference archive (e.g. [CNV_SV_ref_GRCh37d5_brass6+.tar.gz][ftp-ref]) -1. VAGrENT (annotation) reference archive (e.g. [VAGrENT_ref_GRCh37d5_ensembl_75.tar.gz][ftp-ref]) -1. Subclonal reference archive ([SUBCL_ref_GRCh37d5.tar.gz][ftp-ref]) +2. Normal BAM file +3. Core reference archive (e.g. [core_ref_GRCh37d5.tar.gz][ftp-ref]) +4. WXS reference archive (e.g. [SNV_INDEL_ref_GRCh37d5.tar.gz][ftp-ref]) +5. WGS reference archive (e.g. [CNV_SV_ref_GRCh37d5_brass6+.tar.gz][ftp-ref]) +6. VAGrENT (annotation) reference archive (e.g. [VAGrENT_ref_GRCh37d5_ensembl_75.tar.gz][ftp-ref]) +7. Subclonal reference archive ([SUBCL_ref_GRCh37d5.tar.gz][ftp-ref]) * Only needed if `skipbb` is `false` -1. QC reference archive (e.g. [qcGenotype_GRCh37d5.tar.gz][ftp-ref]) +8. QC reference archive (e.g. [qcGenotype_GRCh37d5.tar.gz][ftp-ref]) Inputs 1&2 are expected to have been mapped using [dockstore-cgpmap][dockstore-cgpmap] @@ -56,12 +52,12 @@ your own reference files. Much of this information is available on the individu pages (or the subsequently linked protocols papers). * Specific to dockstore-cgpwgs: - * [BRASS][brass-wiki] - * [ascatNgs][ascatngs-wiki] + * [BRASS][brass-wiki] + * [ascatNgs][ascatngs-wiki] * Inherited from dockstore-cgpwxs: - * [cgpCaVEManWrapper][caveman-wiki] - * [cgpPindel][cgppindel-wiki] - * [VAGrENT][vagrent-wiki] + * [cgpCaVEManWrapper][caveman-wiki] + * [cgpPindel][cgppindel-wiki] + * [VAGrENT][vagrent-wiki] ### Usable Cores @@ -80,54 +76,18 @@ If not set detects available cores on system. All of the tools installed as part of [dockstore-cgpmap][dockstore-cgpmap] and [dockstore-cgpwxs][dockstore-cgpwxs] and the above packages are available for direct use. -``` -export CGPWGS_VER=X.X.X -docker pull quay.io/wtsicgp/dockstore-cgpwgs:$CGPWGS_VER -docker --rm -ti [--volume ...] quay.io/wtsicgp/dockstore-cgpwgs:$CGPWGS_VER bash -``` +See the [docker guide in the wiki][cgpmap-wiki-docker] for more details. ### Singularity -The resulting docker container has been tested with Singularity. The command to exec is: +The resulting docker container has been tested with Singularity. -``` -ds-cgpwgs.pl -h -``` - -Expected use would be along the lines of: - -``` -export CGPWGS_VER=X.X.X -singularity pull docker://quay.io/wtsicgp/dockstore-cgpwgs:$CGPWGS_VER - -singularity exec\ - --workdir /.../workspace \ - --home /.../workspace:/home \ - --bind /.../ref/human:/var/spool/ref:ro \ - --bind /.../example_data/cgpwgs:/var/spool/data:ro \ - dockstore-cgpwgs-${CGPWGS_VER}.simg \ - ds-cgpwgs.pl \ - -reference /var/spool/ref/core_ref_GRCh37d5.tar.gz \ - -annot /var/spool/ref/VAGrENT_ref_GRCh37d5_ensembl_75.tar.gz \ - -snv_indel /var/spool/ref/SNV_INDEL_ref_GRCh37d5-fragment.tar.gz \ - -tumour /var/spool/data/COLO-829_ex.cram \ - ... -``` - -For a system automatically attaching _all local mount points_ (not default singularity behaviour) -you need not specify any `exec` params (workdir, home, bind) but you should specify the `-outdir` -option for `ds-cgpwgs.pl` to prevent data being written to your home directory. - -By default results are written to the home directory of the container so ensure you bind -a large volume and set the `-home` variable. As indicated above the location can be overridden -via the options of `ds-cgpwgs.pl` +See the [docker guide in the wiki][cgpmap-wiki-singularity] for more details. ## Verifying your deployment The `examples/` tree contains test json files populated with data that can be used to verify the -tool. More details can be found [here](examples/README.md). - -The `expected/` tree contains the expected output for each tool. More details can be found [here](expected/README.md). +tool. ## Example data @@ -148,7 +108,7 @@ will need to be manually cleaned to keep the repo size down. Activate the hooks with -``` +```bash git config core.hooksPath git-hooks ``` @@ -157,21 +117,19 @@ git config core.hooksPath git-hooks This project is maintained using HubFlow. 1. Make appropriate changes -1. Build image locally -1. Run all example inputs and verify any changes are acceptable -1. Update `expected/` tree with output of last step -1. Bump version in `Dockerfile` and `Dockstore.cwl` -1. Push changes -1. Check state on Travis -1. Update expected datasets -1. Generate the release (add notes to GitHub) -1. Confirm that image has been built on [quay.io][quay-builds] -1. Update the [dockstore][dockstore-cgpwgs] entry, see [their docs][dockstore-get-started]. +2. Build image locally +3. Run all example inputs and verify any changes are acceptable +4. Bump version in `Dockerfile` and `Dockstore.cwl` +5. Push changes +6. Check state on Travis +7. Generate the release (add notes to GitHub) +8. Confirm that image has been built on [quay.io][quay-builds] +9. Update the [dockstore][dockstore-cgpwgs] entry, see [their docs][dockstore-get-started]. ## LICENCE -``` -Copyright (c) 2017-2018 Genome Research Ltd. +```none +Copyright (c) 2017-2019 Genome Research Ltd. Author: Cancer Genome Project @@ -208,6 +166,8 @@ identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, [caveman-wiki]: https://github.com/cancerit/cgpCaVEManWrapper/wiki [ascatngs-wiki]: https://github.com/cancerit/ascatNgs/wiki [vagrent-wiki]: https://github.com/cancerit/VAGrENT/wiki +[cgpmap-wiki-docker]: https://github.com/cancerit/dockstore-cgpwgs/wiki/Running-under-docker +[cgpmap-wiki-singularity]: https://github.com/cancerit/dockstore-cgpwgs/wiki/Running-under-singularity [travis-base]: https://travis-ci.org/cancerit/dockstore-cgpwgs diff --git a/build/opt-build.sh b/build/opt-build.sh index 4c083d9..5feffe7 100644 --- a/build/opt-build.sh +++ b/build/opt-build.sh @@ -9,7 +9,7 @@ fi set -u ### alleleCount -VER_ALLELECOUNT="v4.0.0" +VER_ALLELECOUNT="v4.0.2" ### cgpNgsQc VER_CGPNGSQC="v1.5.1" @@ -23,13 +23,10 @@ SRC_ASCAT="https://raw.githubusercontent.com/Crick-CancerGenomics/ascat/v2.5.1/A VER_GRASS="v2.1.1" ### BRASS -VER_BRASS="v6.1.2" +VER_BRASS="v6.2.1" SOURCE_BLAT="http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip" SRC_FASTA36="https://github.com/wrpearson/fasta36/archive/fasta-v36.3.8g.tar.gz" -### cgpBattenberg -VER_CGPBB="v3.3.0" - if [ "$#" -lt "1" ] ; then echo "Please provide an installation path such as /opt/ICGC" exit 1 @@ -220,21 +217,6 @@ if [ ! -e $SETUP_DIR/BRASS.success ]; then touch $SETUP_DIR/BRASS.success fi -### cgpBattenberg -if [ ! -e $SETUP_DIR/cgpBB.success ]; then - curl -sSL --retry 10 https://github.com/cancerit/cgpBattenberg/archive/${VER_CGPBB}.tar.gz > distro.tar.gz - rm -rf distro/* - tar --strip-components 1 -C distro -xzf distro.tar.gz - cd distro/Rsupport - ./setupR.sh $INST_PATH - cd $SETUP_DIR/distro/perl - cpanm --no-interactive --notest --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps . - cpanm -v --no-interactive --mirror http://cpan.metacpan.org -l $INST_PATH . - cd $SETUP_DIR - rm -rf distro.* distro/* - touch $SETUP_DIR/cgpBB.success -fi - cd $HOME rm -rf $SETUP_DIR diff --git a/build/rlib-build.R b/build/rlib-build.R index dddaab1..65ecce7 100644 --- a/build/rlib-build.R +++ b/build/rlib-build.R @@ -28,12 +28,4 @@ ipak(c("poweRlaw")) ipak(c("zlibbioc")) ipak(c("RColorBrewer")) -# add for BB -ipak(c("stringi")) -ipak(c("readr")) -ipak(c("doParallel")) -ipak(c("ggplot2")) -ipak(c("gridExtra")) -ipak(c("gtools")) - -install_github("sb43/copynumber", ref="f1688edc154f1a0e3aacf7781090afe02882f623") +install_github("Irrationone/copynumber", ref="87d2663fe6b11c03cf6006b4ee9ed70450eacb5a") diff --git a/cwls/cgpwgs.cwl b/cwls/cgpwgs.cwl index 1c63db0..c907065 100644 --- a/cwls/cgpwgs.cwl +++ b/cwls/cgpwgs.cwl @@ -25,7 +25,7 @@ doc: | requirements: - class: DockerRequirement - dockerPull: "quay.io/wtsicgp/dockstore-cgpwgs:2.0.2" + dockerPull: "quay.io/wtsicgp/dockstore-cgpwgs:2.1.0" hints: - class: ResourceRequirement @@ -62,13 +62,6 @@ inputs: prefix: -cnv_sv separate: true - subcl: - type: File - doc: "Supporting files for allele counts used by Battenberg Subclonal CNV analysis" - inputBinding: - prefix: -subcl - separate: true - qcset: type: File doc: "Supporting files for QC tools" @@ -134,13 +127,6 @@ inputs: separate: true shellQuote: true - skipbb: - type: boolean? - doc: "Skip Battenberg allele counts" - inputBinding: - prefix: -skipbb - separate: true - skipqc: type: boolean? doc: "Disable genotype and verifyBamID steps" diff --git a/examples/cgpwgs/bam_bai.json b/examples/cgpwgs/bam_bai.json index fd60c16..89b58a8 100644 --- a/examples/cgpwgs/bam_bai.json +++ b/examples/cgpwgs/bam_bai.json @@ -15,10 +15,6 @@ "path": "http://ftp.sanger.ac.uk/pub/cancer/dockstore/human/CNV_SV_ref_GRCh37d5_brass6+.tar.gz", "class": "File" }, - "subcl": { - "path": "http://ftp.sanger.ac.uk/pub/cancer/dockstore/human/SUBCL_ref_GRCh37d5.tar.gz", - "class": "File" - }, "qcset": { "path": "http://ftp.sanger.ac.uk/pub/cancer/dockstore/human/qcGenotype_GRCh37d5.tar.gz", "class": "File" @@ -43,7 +39,6 @@ "species": "human", "assembly": "GRCh37d5", "cavereads": 800000, - "skipbb": true, "result_archive": { "path": "/tmp/result_WGS.tar.gz", "class": "File" diff --git a/examples/cgpwgs/bam_bai_pu_pl.json b/examples/cgpwgs/bam_bai_pu_pl.json index 3cbe4ee..aa82ef4 100644 --- a/examples/cgpwgs/bam_bai_pu_pl.json +++ b/examples/cgpwgs/bam_bai_pu_pl.json @@ -15,10 +15,6 @@ "path": "http://ftp.sanger.ac.uk/pub/cancer/dockstore/human/CNV_SV_ref_GRCh37d5_brass6+.tar.gz", "class": "File" }, - "subcl": { - "path": "http://ftp.sanger.ac.uk/pub/cancer/dockstore/human/SUBCL_ref_GRCh37d5.tar.gz", - "class": "File" - }, "qcset": { "path": "http://ftp.sanger.ac.uk/pub/cancer/dockstore/human/qcGenotype_GRCh37d5.tar.gz", "class": "File" @@ -43,7 +39,6 @@ "species": "human", "assembly": "GRCh37d5", "cavereads": 800000, - "skipbb": true, "purity": 0.99, "ploidy": 2, "result_archive": { diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829-BL/contamination/COLO-829-BL.depthRG b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829-BL/contamination/COLO-829-BL.depthRG deleted file mode 100644 index 7dc0d13..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829-BL/contamination/COLO-829-BL.depthRG +++ /dev/null @@ -1,13468 +0,0 @@ -#RG DEPTH #SNPs %SNPs %CUMUL -2649 200 0 0.00000 0.00000 -2649 199 0 0.00000 0.00000 -2649 198 0 0.00000 0.00000 -2649 197 0 0.00000 0.00000 -2649 196 0 0.00000 0.00000 -2649 195 0 0.00000 0.00000 -2649 194 0 0.00000 0.00000 -2649 193 0 0.00000 0.00000 -2649 192 0 0.00000 0.00000 -2649 191 0 0.00000 0.00000 -2649 190 0 0.00000 0.00000 -2649 189 0 0.00000 0.00000 -2649 188 0 0.00000 0.00000 -2649 187 0 0.00000 0.00000 -2649 186 0 0.00000 0.00000 -2649 185 0 0.00000 0.00000 -2649 184 0 0.00000 0.00000 -2649 183 0 0.00000 0.00000 -2649 182 0 0.00000 0.00000 -2649 181 0 0.00000 0.00000 -2649 180 0 0.00000 0.00000 -2649 179 0 0.00000 0.00000 -2649 178 0 0.00000 0.00000 -2649 177 0 0.00000 0.00000 -2649 176 0 0.00000 0.00000 -2649 175 0 0.00000 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0.00000 9077.09 9077.09 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2737 NA 35283 15358 0.44 0.00000 6809.59 6809.59 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2739 NA 35283 21685 0.61 0.00000 9419.21 9419.21 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2741 NA 35283 21094 0.60 0.00000 9062.19 9062.19 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2743 NA 35283 20274 0.57 0.00000 8912.35 8912.35 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2745 NA 35283 21927 0.62 0.00000 9519.33 9519.33 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2747 NA 35283 22450 0.64 0.00000 9584.08 9584.08 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2749 NA 35283 21377 0.61 0.00000 9295.24 9295.24 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2751 NA 35283 22390 0.63 0.00000 9562.52 9562.52 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2753 NA 35283 19785 0.56 0.00000 8642.89 8642.89 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2755 NA 35283 21633 0.61 0.00000 9430.88 9430.88 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2757 NA 35283 22485 0.64 0.00000 9681.00 9681.00 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2759 NA 35283 22527 0.64 0.00000 9740.99 9740.99 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2762 NA 35283 24958 0.71 0.00000 10649.54 10649.54 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2764 NA 35283 24581 0.70 0.00000 10365.04 10365.04 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2767 NA 35283 24253 0.69 0.00000 10348.05 10348.05 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2769 NA 35283 24453 0.69 0.00000 10321.45 10321.45 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2772 NA 35283 23534 0.67 0.00000 10112.26 10112.26 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2774 NA 35283 23461 0.66 0.00000 10083.68 10083.68 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2776 NA 35283 24907 0.71 0.00000 10460.70 10460.70 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2779 NA 35283 24558 0.70 0.00000 10413.08 10413.08 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2781 NA 35283 21801 0.62 0.00000 9339.48 9339.48 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2783 NA 35283 23326 0.66 0.00000 9874.64 9874.64 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2785 NA 35283 22665 0.64 0.00000 9652.76 9652.76 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2787 NA 35283 23602 0.67 0.00000 9966.43 9966.43 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2790 NA 35283 23681 0.67 0.00000 10074.88 10074.88 NA NA NA NA NA NA NA NA NA NA -COLO-829-BL 2792 NA 35283 23065 0.65 0.00000 9725.33 9725.33 NA NA NA NA NA NA NA NA NA NA diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829-BL/contamination/COLO-829-BL.selfSM b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829-BL/contamination/COLO-829-BL.selfSM deleted file mode 100644 index 463644d..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829-BL/contamination/COLO-829-BL.selfSM +++ /dev/null @@ -1,2 +0,0 @@ -#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT -COLO-829-BL ALL NA 35283 1489080 42.20 0.00075 336467.25 336532.29 NA NA NA NA NA NA NA NA NA NA diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829-BL/contamination/COLO-829-BL_snps.vcf b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829-BL/contamination/COLO-829-BL_snps.vcf deleted file mode 100644 index cf49e8c..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829-BL/contamination/COLO-829-BL_snps.vcf +++ /dev/null @@ -1,35408 +0,0 @@ -#CHROM POS ID REF ALT QUAL FILTER INFO -1 1017216 rs6667248 A G . PASS AF=0.04188 -1 1311716 rs2649589 G A . PASS AF=0.77138 -1 1778090 rs12126768 T G . PASS AF=0.15348 -1 2069681 rs3753242 C T . PASS AF=0.19781 -1 2234251 rs1496555 A G . PASS AF=0.86161 -1 2328714 rs2645081 A G . PASS AF=0.84304 -1 2546229 rs6684865 G A . PASS AF=0.43266 -1 2831369 rs2606408 T C . PASS AF=0.05865 -1 2919942 rs12022429 G A . PASS AF=0.17887 -1 2974212 rs12057171 T C . PASS AF=0.02565 -1 3080855 rs1798246 A C . PASS AF=0.43709 -1 3138136 rs2817148 A G . PASS AF=0.13715 -1 3220160 rs6670518 A G . PASS AF=0.11327 -1 3256202 rs16824338 G A . PASS AF=0.04755 -1 3337552 rs2493283 T C . PASS AF=0.08286 -1 3494079 rs12080677 A G . PASS AF=0.22687 -1 3607520 rs3765730 G A . PASS AF=0.25503 -1 3696639 rs16824088 C T . PASS AF=0.02402 -1 3751929 rs12093010 G T . PASS AF=0.04990 -1 3999637 rs4654522 C G . PASS AF=0.33273 -1 4039440 rs12758410 C T . PASS AF=0.51987 -1 4111741 rs4553153 C T . PASS AF=0.25766 -1 4158734 rs12031803 T A . PASS AF=0.03986 -1 4220301 rs7549636 G A . PASS AF=0.24675 -1 4284659 rs903540 T C . PASS AF=0.68878 -1 4343581 rs16838549 G A . PASS AF=0.02398 -1 4370346 rs16838636 C A . PASS AF=0.01553 -1 4395020 rs12046130 G A . PASS AF=0.05761 -1 4426478 rs16838819 A C . PASS AF=0.18149 -1 4457112 rs16838929 C G . PASS AF=0.16709 -1 4482610 rs737324 G C . PASS AF=0.38945 -1 4523410 rs17453664 G A . PASS AF=0.12283 -1 4559484 rs616317 C A . PASS AF=0.07528 -1 4582089 rs518456 T G . PASS AF=0.35263 -1 4617856 rs10799244 T C . PASS AF=0.25289 -1 4657295 rs651695 A T . PASS AF=0.25761 -1 4693931 rs6687814 A G . PASS AF=0.40161 -1 4734514 rs12411035 A G . PASS AF=0.17888 -1 4774438 rs242058 T C . PASS AF=0.87270 -1 4812815 rs381240 A G . PASS AF=0.30488 -1 4853068 rs12408533 A G . PASS AF=0.03817 -1 4897644 rs11576972 G C . PASS AF=0.18922 -1 4958939 rs10915656 A G . PASS AF=0.22449 -1 4986435 rs4529681 G A . PASS AF=0.08583 -1 5011290 rs12403612 C G . PASS AF=0.07067 -1 5048624 rs7541612 T C . PASS AF=0.85640 -1 5088617 rs2169089 A G . PASS AF=0.76304 -1 5151476 rs2199215 T C . PASS AF=0.52212 -1 5198789 rs16840051 C T . PASS AF=0.34230 -1 5247355 rs10492931 G A . PASS AF=0.45884 -1 5303371 rs480807 G A . PASS AF=0.64359 -1 5330286 rs494138 C T . PASS AF=0.46626 -1 5362292 rs9439551 C G . PASS AF=0.38029 -1 5410542 rs4129058 C T . PASS AF=0.54484 -1 5532101 rs12566922 T G . PASS AF=0.14638 -1 5572076 rs10796398 G A . PASS AF=0.22742 -1 5625929 rs7523214 C G . PASS AF=0.05431 -1 5645712 rs4845805 G A . PASS AF=0.39912 -1 5684440 rs945321 C A . PASS AF=0.16142 -1 5718367 rs17028547 A C . PASS AF=0.02072 -1 5750582 rs770710 A T . PASS AF=0.16094 -1 5813724 rs12061902 T C . PASS AF=0.17633 -1 5902086 rs11579676 C T . PASS AF=0.21427 -1 5925955 rs12737596 T C . PASS AF=0.04300 -1 5985072 rs1011994 C T . PASS AF=0.14861 -1 6059322 rs7524865 G A . PASS AF=0.14348 -1 6141261 rs6701690 C G . PASS AF=0.10958 -1 6272813 rs2294711 C T . PASS AF=0.11485 -1 6416104 rs3789470 T C . PASS AF=0.10013 -1 6581283 rs12410405 C G . PASS AF=0.20773 -1 6713114 rs2235564 C T . PASS AF=0.31874 -1 6817343 rs17027008 T A . PASS AF=0.13993 -1 6927752 rs11120780 A G . PASS AF=0.63959 -1 7018719 rs11120797 A G . PASS AF=0.03063 -1 7089029 rs17030160 A C . PASS AF=0.01558 -1 7146809 rs9434834 T C . PASS AF=0.15858 -1 7214374 rs13376128 G T . PASS AF=0.22414 -1 7297400 rs7521056 A T . PASS AF=0.11816 -1 7336978 rs4908615 T A . PASS AF=0.43213 -1 7406419 rs4908456 T C . PASS AF=0.34129 -1 7449971 rs7524314 G A . PASS AF=0.29214 -1 7527996 rs1201529 T C . PASS AF=0.52139 -1 7554982 rs1725269 C T . PASS AF=0.70066 -1 7626995 rs17031145 C A . PASS AF=0.05192 -1 7697179 rs6661496 A T . PASS AF=0.09450 -1 7795554 rs4908688 C T . PASS AF=0.18933 -1 7850081 rs10864315 C T . PASS AF=0.26519 -1 7926542 rs504560 A G . PASS AF=0.64277 -1 8000562 rs9657956 C T . PASS AF=0.05221 -1 8161850 rs11487884 A G . PASS AF=0.08060 -1 8206326 rs6577473 C A . PASS AF=0.59929 -1 8273177 rs6683603 T G . PASS AF=0.32833 -1 8329710 rs2661869 C T . PASS AF=0.63665 -1 8457623 rs1443929 G T . PASS AF=0.15060 -1 8612104 rs6577499 G C . PASS AF=0.64178 -1 8767780 rs10864364 C A . PASS AF=0.85979 -1 8899305 rs6577532 C T . PASS AF=0.81602 -1 8993867 rs7417097 G A . PASS AF=0.30485 -1 9045124 rs7513804 C T . PASS AF=0.71809 -1 9116743 rs12080175 T C . PASS AF=0.30975 -1 9219383 rs6577556 T C . PASS AF=0.20481 -1 9292082 rs3753271 C T . PASS AF=0.30014 -1 9368209 rs1294040 G A . PASS AF=0.64682 -1 9417946 rs9435244 G A . PASS AF=0.10350 -1 9495587 rs9726405 T C . PASS AF=0.17077 -1 9650571 rs6669846 C T . PASS AF=0.02455 -1 9784423 rs11121484 C T . PASS AF=0.21830 -1 10013014 rs7516611 A C . PASS AF=0.15632 -1 10232200 rs17034569 C T . PASS AF=0.08874 -1 10353112 rs10492972 T C . PASS AF=0.32968 -1 10502710 rs2847337 A G . PASS AF=0.81899 -1 10591104 rs12090079 T C . PASS AF=0.07608 -1 10627542 rs12033275 G T . PASS AF=0.20859 -1 10726689 rs284321 G A . PASS AF=0.12132 -1 10832861 rs205474 C T . PASS AF=0.57717 -1 10929298 rs1281001 A G . PASS AF=0.59128 -1 11034817 rs9659356 A G . PASS AF=0.29462 -1 11191232 rs12732063 G A . PASS AF=0.01854 -1 11289161 rs2076655 G A . PASS AF=0.57495 -1 11401745 rs2982384 G A . PASS AF=0.37641 -1 11461601 rs6671983 G A . PASS AF=0.36952 -1 11507303 rs3010220 G A . PASS AF=0.02134 -1 11567190 rs2817637 C T . PASS AF=0.46179 -1 11647669 rs2817644 C T . PASS AF=0.31047 -1 11749908 rs6694489 C T . PASS AF=0.19377 -1 11828319 rs4845881 G A . PASS AF=0.65428 -1 11896654 rs198403 G A . PASS AF=0.12652 -1 11960394 rs17346334 T C . PASS AF=0.06100 -1 12117901 rs6665486 A G . PASS AF=0.46139 -1 12194612 rs1148471 G A . PASS AF=0.47178 -1 12249770 rs548580 G A . PASS AF=0.19639 -1 12418700 rs10864552 T C . PASS AF=0.94679 -1 12615069 rs6659122 G T . PASS AF=0.13976 -1 12672536 rs12046693 G C . PASS AF=0.21400 -1 12765166 rs4568844 C T . PASS AF=0.75593 -1 12813522 rs4548455 C T . PASS AF=0.05027 -1 13008676 rs3928862 G A . PASS AF=0.16698 -1 13841055 rs2990683 T C . PASS AF=0.65144 -1 13909142 rs355023 A C . PASS AF=0.63583 -1 13948047 rs12085273 G T . PASS AF=0.02610 -1 14043026 rs12049438 G A . PASS AF=0.17276 -1 14119085 rs1203642 T C . PASS AF=0.17732 -1 14150992 rs2697962 T C . PASS AF=0.82785 -1 14216150 rs17350970 C T . PASS AF=0.03696 -1 14252247 rs1534946 A G . PASS AF=0.12197 -1 14278991 rs7532844 T A . PASS AF=0.10033 -1 14313274 rs12728009 A G . PASS AF=0.18096 -1 14346018 rs7515012 C T . PASS AF=0.18178 -1 14380326 rs7519048 G C . PASS AF=0.14984 -1 14441384 rs7519796 A G . PASS AF=0.73920 -1 14474715 rs11586283 T C . PASS AF=0.33907 -1 14509276 rs577987 A G . PASS AF=0.15488 -1 14586318 rs10754915 T C . PASS AF=0.94610 -1 14655424 rs16853960 G A . PASS AF=0.04361 -1 14726096 rs820668 T C . PASS AF=0.96262 -1 14782380 rs6682103 T G . PASS AF=0.57814 -1 14811781 rs2480063 G A . PASS AF=0.45767 -1 14859579 rs7540545 T C . PASS AF=0.39903 -1 14919895 rs664747 G A . PASS AF=0.46653 -1 14981240 rs7530538 T C . PASS AF=0.59303 -1 15047171 rs10754867 G A . PASS AF=0.70954 -1 15089767 rs4543785 C T . PASS AF=0.38483 -1 15136508 rs3916544 C T . PASS AF=0.24768 -1 15192916 rs4661539 C A . PASS AF=0.44374 -1 15256903 rs12141312 T A . PASS AF=0.40972 -1 15295333 rs10927602 A G . PASS AF=0.51805 -1 15333053 rs4633284 C G . PASS AF=0.24429 -1 15360721 rs938255 C T . PASS AF=0.75659 -1 15431657 rs494983 G T . PASS AF=0.60133 -1 15500332 rs16851358 C T . PASS AF=0.16298 -1 15528667 rs17382617 G A . PASS AF=0.03972 -1 15566699 rs10927744 G A . PASS AF=0.87298 -1 15631649 rs17377023 G A . PASS AF=0.03249 -1 15701116 rs10927776 C T . PASS AF=0.02729 -1 15759547 rs6700655 T A . PASS AF=0.38681 -1 15843244 rs2042369 G A . PASS AF=0.21551 -1 15960608 rs11808281 G A . PASS AF=0.02708 -1 16087824 rs12091731 C T . PASS AF=0.25773 -1 16282776 rs4661346 G C . PASS AF=0.15663 -1 16379416 rs12015135 A C . PASS AF=0.18019 -1 16534646 rs221058 C G . PASS AF=0.18944 -1 16716374 rs612727 T C . PASS AF=0.73533 -1 16814994 rs156851 C T . PASS AF=0.93350 -1 17290058 rs6696928 A G . PASS AF=0.94176 -1 17386104 rs12404121 C T . PASS AF=0.55366 -1 17409241 rs2235925 G A . PASS AF=0.41606 -1 17465174 rs2746486 A G . PASS AF=0.53898 -1 17514734 rs3003464 C G . PASS AF=0.25143 -1 17557837 rs3003409 A C . PASS AF=0.39339 -1 17595925 rs17458091 T C . PASS AF=0.08699 -1 17655407 rs1748041 C T . PASS AF=0.63610 -1 17694701 rs1204890 T G . PASS AF=0.28934 -1 17785736 rs2428740 C T . PASS AF=0.34500 -1 17903298 rs6702679 G A . PASS AF=0.32566 -1 18003946 rs6665721 C T . PASS AF=0.02171 -1 18079812 rs12136469 C T . PASS AF=0.22986 -1 18143674 rs508571 C T . PASS AF=0.33696 -1 18201318 rs563835 T C . PASS AF=0.48431 -1 18246140 rs12073092 T A . PASS AF=0.31540 -1 18282095 rs1192583 G A . PASS AF=0.93892 -1 18317841 rs12726822 G A . PASS AF=0.20157 -1 18343106 rs12058837 G T . PASS AF=0.14041 -1 18374838 rs4920416 T C . PASS AF=0.99900 -1 18428766 rs1342572 G A . PASS AF=0.94886 -1 18468789 rs1455913 G A . PASS AF=0.29995 -1 18504792 rs4920448 T C . PASS AF=0.07059 -1 18553632 rs17489003 T C . PASS AF=0.21247 -1 18586815 rs402642 T C . PASS AF=0.37700 -1 18633357 rs12127986 G T . PASS AF=0.24380 -1 18678170 rs16861827 C T . PASS AF=0.11961 -1 18707373 rs10492995 A C . PASS AF=0.14486 -1 18761893 rs1850750 C T . PASS AF=0.12576 -1 18797703 rs2992736 A G . PASS AF=0.43313 -1 18839394 rs2294656 C T . PASS AF=0.27825 -1 18913558 rs4920334 T C . PASS AF=0.31500 -1 18995326 rs12141588 C T . PASS AF=0.02624 -1 19049615 rs2236817 C A . PASS AF=0.13805 -1 19094790 rs7545724 A G . PASS AF=0.05729 -1 19131080 rs7418296 G A . PASS AF=0.13208 -1 19203997 rs2230705 C G . PASS AF=0.64065 -1 19323050 rs6690097 G C . PASS AF=0.19334 -1 19400626 rs3748762 T C . PASS AF=0.04243 -1 19442508 rs4911974 C T . PASS AF=0.73542 -1 19564037 rs710879 C T . PASS AF=0.21175 -1 19645673 rs4912069 G A . 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0.00914 0.94001 -ALL 36 191 0.00914 0.94915 -ALL 35 158 0.00756 0.95672 -ALL 34 148 0.00709 0.96381 -ALL 33 118 0.00565 0.96945 -ALL 32 94 0.00450 0.97396 -ALL 31 93 0.00445 0.97841 -ALL 30 70 0.00335 0.98176 -ALL 29 68 0.00326 0.98501 -ALL 28 68 0.00326 0.98827 -ALL 27 51 0.00244 0.99071 -ALL 26 37 0.00177 0.99248 -ALL 25 30 0.00144 0.99392 -ALL 24 24 0.00115 0.99507 -ALL 23 22 0.00105 0.99612 -ALL 22 14 0.00067 0.99679 -ALL 21 13 0.00062 0.99741 -ALL 20 10 0.00048 0.99789 -ALL 19 10 0.00048 0.99837 -ALL 18 4 0.00019 0.99856 -ALL 17 1 0.00005 0.99861 -ALL 16 3 0.00014 0.99876 -ALL 15 2 0.00010 0.99885 -ALL 14 2 0.00010 0.99895 -ALL 13 1 0.00005 0.99899 -ALL 12 1 0.00005 0.99904 -ALL 11 1 0.00005 0.99909 -ALL 10 2 0.00010 0.99919 -ALL 9 0 0.00000 0.99919 -ALL 8 2 0.00010 0.99928 -ALL 7 1 0.00005 0.99933 -ALL 6 0 0.00000 0.99933 -ALL 5 0 0.00000 0.99933 -ALL 4 1 0.00005 0.99938 -ALL 3 0 0.00000 0.99938 -ALL 2 1 0.00005 0.99943 -ALL 1 1 0.00005 0.99947 -ALL 0 11 0.00053 1.00000 diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829.log b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829.log deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829.log +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829.selfRG b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829.selfRG deleted file mode 100644 index 383f6de..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829.selfRG +++ /dev/null @@ -1,104 +0,0 @@ -#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT -COLO-829 2650 NA 20887 14834 0.71 0.00000 6244.71 6244.71 NA NA NA NA NA NA NA NA NA NA -COLO-829 2652 NA 20887 14397 0.69 0.00000 6102.14 6102.14 NA NA NA NA NA NA NA NA NA NA -COLO-829 2654 NA 20887 13808 0.66 0.00000 5928.59 5928.59 NA NA NA NA NA NA NA NA NA NA -COLO-829 2656 NA 20887 14978 0.72 0.00000 6468.85 6468.85 NA NA NA NA NA NA NA NA NA NA -COLO-829 2658 NA 20887 14855 0.71 0.00000 6317.03 6317.03 NA NA NA NA NA NA NA NA NA NA -COLO-829 2659 NA 20887 14404 0.69 0.00000 6183.35 6183.35 NA NA NA NA NA NA NA NA NA NA -COLO-829 2661 NA 20887 13627 0.65 0.00000 5836.79 5836.79 NA NA NA NA NA NA NA NA NA NA -COLO-829 2663 NA 20887 14729 0.71 0.00000 6123.33 6123.33 NA NA NA NA NA NA NA NA NA NA -COLO-829 2665 NA 20887 14894 0.71 0.00000 6314.45 6314.45 NA NA NA NA NA NA NA NA NA NA -COLO-829 2667 NA 20887 13545 0.65 0.00000 5870.44 5870.44 NA NA NA NA NA NA NA NA NA NA -COLO-829 2669 NA 20887 14893 0.71 0.00000 6341.18 6341.18 NA NA NA NA NA NA NA NA NA NA -COLO-829 2671 NA 20887 14560 0.70 0.00000 6215.95 6215.95 NA NA NA NA NA NA NA NA NA NA -COLO-829 2673 NA 20887 14430 0.69 0.00000 6142.12 6142.12 NA NA NA NA NA NA NA NA NA NA -COLO-829 2675 NA 20887 15005 0.72 0.00000 6317.80 6317.80 NA NA NA NA NA NA NA NA NA NA -COLO-829 2677 NA 20887 11195 0.54 0.00000 4821.94 4821.94 NA NA NA NA NA NA NA NA NA NA -COLO-829 2679 NA 20887 12557 0.60 0.00000 5226.94 5226.94 NA NA NA NA NA NA NA NA NA NA -COLO-829 2681 NA 20887 11783 0.56 0.00000 5125.32 5125.32 NA NA NA NA NA NA NA NA NA NA -COLO-829 2684 NA 20887 9130 0.44 0.00000 3939.40 3939.40 NA NA NA NA NA NA NA NA NA NA -COLO-829 2685 NA 20887 12619 0.60 0.00000 5353.48 5353.48 NA NA NA NA NA NA NA NA NA NA -COLO-829 2687 NA 20887 9593 0.46 0.00000 4178.21 4178.21 NA NA NA NA NA NA NA NA NA NA -COLO-829 2689 NA 20887 14440 0.69 0.00000 6046.29 6046.29 NA NA NA NA NA NA NA NA NA NA -COLO-829 2691 NA 20887 14524 0.70 0.00000 6161.65 6161.65 NA NA NA NA NA NA NA NA NA NA -COLO-829 2693 NA 20887 14061 0.67 0.00000 5959.91 5959.91 NA NA NA NA NA NA NA NA NA NA -COLO-829 2695 NA 20887 14224 0.68 0.00000 5855.61 5855.61 NA NA NA NA NA NA NA NA NA NA -COLO-829 2697 NA 20887 13982 0.67 0.00000 5927.73 5927.73 NA NA NA NA NA NA NA NA NA NA -COLO-829 2699 NA 20887 13570 0.65 0.00000 5750.99 5750.99 NA NA NA NA NA NA NA NA NA NA -COLO-829 2701 NA 20887 13492 0.65 0.00000 5753.60 5753.60 NA NA NA NA NA NA NA NA NA NA -COLO-829 2702 NA 20887 13177 0.63 0.00000 5609.36 5609.36 NA NA NA NA NA NA NA NA NA NA -COLO-829 2704 NA 20887 13386 0.64 0.00000 5653.54 5653.54 NA NA NA NA NA NA NA NA NA NA -COLO-829 2706 NA 20887 12685 0.61 0.00000 5357.31 5357.31 NA NA NA NA NA NA NA NA NA NA -COLO-829 2708 NA 20887 13722 0.66 0.00000 5920.17 5920.17 NA NA NA NA NA NA NA NA NA NA -COLO-829 2710 NA 20887 11511 0.55 0.00000 4977.11 4977.11 NA NA NA NA NA NA NA NA NA NA -COLO-829 2711 NA 20887 12749 0.61 0.00000 5432.92 5432.92 NA NA NA NA NA NA NA NA NA NA -COLO-829 2713 NA 20887 11114 0.53 0.00000 4788.91 4788.91 NA NA NA NA NA NA NA NA NA NA -COLO-829 2715 NA 20887 13869 0.66 0.00000 5932.05 5932.05 NA NA NA NA NA NA NA NA NA NA -COLO-829 2717 NA 20887 12957 0.62 0.00000 5632.26 5632.26 NA NA NA NA NA NA NA NA NA NA -COLO-829 2719 NA 20887 12715 0.61 0.00000 5461.20 5461.20 NA NA NA NA NA NA NA NA NA NA -COLO-829 2721 NA 20887 13061 0.63 0.00000 5702.90 5702.90 NA NA NA NA NA NA NA NA NA NA -COLO-829 2723 NA 20887 12678 0.61 0.00000 5362.88 5362.88 NA NA NA NA NA NA NA NA NA NA -COLO-829 2725 NA 20887 11094 0.53 0.00000 4888.74 4888.74 NA NA NA NA NA NA NA NA NA NA -COLO-829 2726 NA 20887 11057 0.53 0.00000 4751.95 4751.95 NA NA NA NA NA NA NA NA NA NA -COLO-829 2728 NA 20887 11881 0.57 0.00000 5076.45 5076.45 NA NA NA NA NA NA NA NA NA NA -COLO-829 2730 NA 20887 12664 0.61 0.00000 5535.98 5535.98 NA NA NA NA NA NA NA NA NA NA -COLO-829 2732 NA 20887 13298 0.64 0.00000 5730.10 5730.10 NA NA NA NA NA NA NA NA NA NA -COLO-829 2734 NA 20887 12746 0.61 0.00000 5516.28 5516.28 NA NA NA NA NA NA NA NA NA NA -COLO-829 2736 NA 20887 11995 0.57 0.00000 5134.69 5134.69 NA NA NA NA NA NA NA NA NA NA -COLO-829 2738 NA 20887 12300 0.59 0.00000 5144.32 5144.32 NA NA NA NA NA NA NA NA NA NA -COLO-829 2740 NA 20887 12851 0.62 0.00000 5570.09 5570.09 NA NA NA NA NA NA NA NA NA NA -COLO-829 2742 NA 20887 12823 0.61 0.00000 5413.96 5413.96 NA NA NA NA NA NA NA NA NA NA -COLO-829 2744 NA 20887 13331 0.64 0.00000 5782.94 5782.94 NA NA NA NA NA NA NA NA NA NA -COLO-829 2746 NA 20887 14345 0.69 0.00000 6073.73 6073.73 NA NA NA NA NA NA NA NA NA NA -COLO-829 2748 NA 20887 13276 0.64 0.00000 5641.28 5641.28 NA NA NA NA NA NA NA NA NA NA -COLO-829 2750 NA 20887 14379 0.69 0.00000 6132.25 6132.25 NA NA NA NA NA NA NA NA NA NA -COLO-829 2752 NA 20887 14082 0.67 0.00000 5936.96 5936.96 NA NA NA NA NA NA NA NA NA NA -COLO-829 2754 NA 20887 14143 0.68 0.00000 5973.32 5973.32 NA NA NA NA NA NA NA NA NA NA -COLO-829 2756 NA 20887 13849 0.66 0.00000 5866.94 5866.94 NA NA NA NA NA NA NA NA NA NA -COLO-829 2758 NA 20887 14477 0.69 0.00000 6251.25 6251.25 NA NA NA NA NA NA NA NA NA NA -COLO-829 2760 NA 20887 11918 0.57 0.00000 5041.71 5041.71 NA NA NA NA NA NA NA NA NA NA -COLO-829 2761 NA 20887 13080 0.63 0.00000 5550.09 5550.09 NA NA NA NA NA NA NA NA NA NA -COLO-829 2763 NA 20887 11502 0.55 0.00000 4987.49 4987.49 NA NA NA NA NA NA NA NA NA NA -COLO-829 2765 NA 20887 10228 0.49 0.00000 4393.78 4393.78 NA NA NA NA NA NA NA NA NA NA -COLO-829 2766 NA 20887 12094 0.58 0.00000 5174.67 5174.67 NA NA NA NA NA NA NA NA NA NA -COLO-829 2768 NA 20887 10570 0.51 0.00000 4587.56 4587.56 NA NA NA NA NA NA NA NA NA NA -COLO-829 2770 NA 20887 11795 0.56 0.00000 4976.39 4976.39 NA NA NA NA NA NA NA NA NA NA -COLO-829 2771 NA 20887 11695 0.56 0.00000 5099.75 5099.75 NA NA NA NA NA NA NA NA NA NA -COLO-829 2773 NA 20887 9950 0.48 0.00000 4334.79 4334.79 NA NA NA NA NA NA NA NA NA NA -COLO-829 2775 NA 20887 10000 0.48 0.00000 4376.84 4376.84 NA NA NA NA NA NA NA NA NA NA -COLO-829 2777 NA 20887 13342 0.64 0.00000 5804.90 5804.90 NA NA NA NA NA NA NA NA NA NA -COLO-829 2778 NA 20887 13858 0.66 0.00000 5877.87 5877.87 NA NA NA NA NA NA NA NA NA NA -COLO-829 2780 NA 20887 12794 0.61 0.00000 5446.46 5446.46 NA NA NA NA NA NA NA NA NA NA -COLO-829 2782 NA 20887 13059 0.63 0.00000 5655.49 5655.49 NA NA NA NA NA NA NA NA NA NA -COLO-829 2784 NA 20887 11211 0.54 0.00000 4848.12 4848.12 NA NA NA NA NA NA NA NA NA NA -COLO-829 2786 NA 20887 11787 0.56 0.00000 5123.81 5123.81 NA NA NA NA NA NA NA NA NA NA -COLO-829 2788 NA 20887 13692 0.66 0.00000 5864.90 5864.90 NA NA NA NA NA NA NA NA NA NA -COLO-829 2789 NA 20887 13025 0.62 0.00000 5622.95 5622.95 NA NA NA NA NA NA NA NA NA NA -COLO-829 2791 NA 20887 14174 0.68 0.00000 5962.52 5962.52 NA NA NA NA NA NA NA NA NA NA -COLO-829 2793 NA 20887 15277 0.73 0.00000 6455.37 6455.37 NA NA NA NA NA NA NA NA NA NA -COLO-829 2794 NA 20887 12709 0.61 0.00000 5530.05 5530.05 NA NA NA NA NA NA NA NA NA NA -COLO-829 2795 NA 20887 14498 0.69 0.00000 6136.42 6136.42 NA NA NA NA NA NA NA NA NA NA -COLO-829 2796 NA 20887 14820 0.71 0.00000 6101.75 6101.75 NA NA NA NA NA NA NA NA NA NA -COLO-829 2797 NA 20887 13987 0.67 0.00000 6004.10 6004.10 NA NA NA NA NA NA NA NA NA NA -COLO-829 2798 NA 20887 14994 0.72 0.00000 6367.85 6367.85 NA NA NA NA NA NA NA NA NA NA -COLO-829 2799 NA 20887 11700 0.56 0.00000 5095.41 5095.41 NA NA NA NA NA NA NA NA NA NA -COLO-829 2800 NA 20887 14581 0.70 0.00000 6280.03 6280.03 NA NA NA NA NA NA NA NA NA NA -COLO-829 2801 NA 20887 10890 0.52 0.00000 4813.41 4813.41 NA NA NA NA NA NA NA NA NA NA -COLO-829 2802 NA 20887 14401 0.69 0.00000 6169.91 6169.91 NA NA NA NA NA NA NA NA NA NA -COLO-829 2803 NA 20887 9380 0.45 0.00000 4123.90 4123.90 NA NA NA NA NA NA NA NA NA NA -COLO-829 2804 NA 20887 12460 0.60 0.00000 5434.13 5434.13 NA NA NA NA NA NA NA NA NA NA -COLO-829 2805 NA 20887 13473 0.65 0.00000 5660.14 5660.14 NA NA NA NA NA NA NA NA NA NA -COLO-829 2806 NA 20887 10204 0.49 0.00000 4553.81 4553.81 NA NA NA NA NA NA NA NA NA NA -COLO-829 2807 NA 20887 9366 0.45 0.00000 4117.81 4117.81 NA NA NA NA NA NA NA NA NA NA -COLO-829 2808 NA 20887 10297 0.49 0.00000 4516.26 4516.26 NA NA NA NA NA NA NA NA NA NA -COLO-829 2809 NA 20887 10244 0.49 0.00000 4561.70 4561.70 NA NA NA NA NA NA NA NA NA NA -COLO-829 76 NA 20887 3979 0.19 0.00000 1899.07 1899.07 NA NA NA NA NA NA NA NA NA NA -COLO-829 77 NA 20887 4180 0.20 0.00000 1879.38 1879.38 NA NA NA NA NA NA NA NA NA NA -COLO-829 78 NA 20887 3241 0.16 0.01277 1465.91 1465.93 NA NA NA NA NA NA NA NA NA NA -COLO-829 81 NA 20887 3829 0.18 0.00000 1760.72 1760.72 NA NA NA NA NA NA NA NA NA NA -COLO-829 994 NA 20887 3297 0.16 0.07082 1444.92 1445.34 NA NA NA NA NA NA NA NA NA NA -COLO-829 995 NA 20887 2891 0.14 0.00000 1279.04 1279.04 NA NA NA NA NA NA NA NA NA NA -COLO-829 996 NA 20887 3304 0.16 0.00000 1497.73 1497.73 NA NA NA NA NA NA NA NA NA NA -COLO-829 997 NA 20887 3409 0.16 0.00000 1465.42 1465.42 NA NA NA NA NA NA NA NA NA NA -COLO-829 998 NA 20887 3280 0.16 0.00000 1437.91 1437.91 NA NA NA NA NA NA NA NA NA NA -COLO-829 999 NA 20887 3364 0.16 0.11522 1471.54 1472.46 NA NA NA NA NA NA NA NA NA NA diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829.selfSM b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829.selfSM deleted file mode 100644 index d673731..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829.selfSM +++ /dev/null @@ -1,2 +0,0 @@ -#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT -COLO-829 ALL NA 20887 1234173 59.09 0.00109 272092.96 272205.96 NA NA NA NA NA NA NA NA NA NA diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829_snps.vcf b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829_snps.vcf deleted file mode 100644 index bbe9eb6..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829/contamination/COLO-829_snps.vcf +++ /dev/null @@ -1,20961 +0,0 @@ -#CHROM POS ID REF ALT QUAL FILTER INFO -1 144551842 rs1699721 C T . PASS AF=0.95000 -1 144945737 rs2996281 G T . PASS AF=0.68029 -1 145041016 rs2799329 G A . PASS AF=0.05000 -2 41404 rs10173732 G A . PASS AF=0.18223 -2 151464 rs381726 T C . PASS AF=0.51279 -2 210076 rs11692330 G C . PASS AF=0.34338 -2 282736 rs6708541 G T . PASS AF=0.67819 -2 355800 rs6740249 T C . PASS AF=0.68073 -2 454860 rs1511324 G A . PASS AF=0.25911 -2 548121 rs2685261 C T . PASS AF=0.73483 -2 589743 rs2683980 G A . PASS AF=0.11729 -2 614168 rs2947411 A G . PASS AF=0.84001 -2 637830 rs13393304 A G . PASS AF=0.87828 -2 669023 rs3187671 C T . PASS AF=0.11917 -2 759749 rs7596247 A G . PASS AF=0.27573 -2 825721 rs4358155 A C . PASS AF=0.85572 -2 877633 rs12466616 G A . PASS AF=0.52501 -2 943250 rs4971346 C T . PASS AF=0.26955 -2 1025239 rs10201045 A G . PASS AF=0.71192 -2 1077718 rs10470000 T C . PASS AF=0.99900 -2 1173710 rs4464311 T C . PASS AF=0.58960 -2 1311760 rs9678456 T C . PASS AF=0.07164 -2 1383237 rs4927650 T G . PASS AF=0.68697 -2 1432599 rs949834 G A . PASS AF=0.08284 -2 1473898 rs11897718 T A . PASS AF=0.22705 -2 1620721 rs12614899 C T . PASS AF=0.20106 -2 1696016 rs2288183 G A . PASS AF=0.62480 -2 1772199 rs13403413 G A . PASS AF=0.25325 -2 1838964 rs6747366 A G . PASS AF=0.50786 -2 1897522 rs12476079 G C . PASS AF=0.08354 -2 1974582 rs1864882 T G . PASS AF=0.51705 -2 2058426 rs6716149 C T . PASS AF=0.04490 -2 2204863 rs12471456 G A . PASS AF=0.28694 -2 2268764 rs6753548 C G . PASS AF=0.64530 -2 2355993 rs2551214 G T . PASS AF=0.57480 -2 2410541 rs2063549 C T . PASS AF=0.25024 -2 2474047 rs1706869 G T . PASS AF=0.08784 -2 2520736 rs1710503 C T . PASS AF=0.61866 -2 2538135 rs17039995 G A . PASS AF=0.02618 -2 2583815 rs10166891 T C . PASS AF=0.17379 -2 2608466 rs17496843 C T . PASS AF=0.17934 -2 2643137 rs7591104 C G . PASS AF=0.38903 -2 2687911 rs1470738 A G . PASS AF=0.61086 -2 2740902 rs9309697 A G . PASS AF=0.86916 -2 2787699 rs4146909 T C . PASS AF=0.67053 -2 2837549 rs11686670 C A . PASS AF=0.24521 -2 2872628 rs876299 A G . 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/dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.caveman.vcf.gz.tbi b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.caveman.vcf.gz.tbi deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.caveman.vcf.gz.tbi +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.logR.bw b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.logR.bw deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.logR.bw +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.minorCn.bw b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.minorCn.bw deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.minorCn.bw +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.rawCn.bw b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.rawCn.bw deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.rawCn.bw +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.segBaf.bw b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.segBaf.bw deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.segBaf.bw +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.segLogR.bw b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.segLogR.bw deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.segLogR.bw +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.totalCn.bw b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.totalCn.bw deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.totalCn.bw +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.txt.gz b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.txt.gz deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.copynumber.txt.gz +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.germline.png b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.germline.png deleted file mode 100644 index dd54d3e..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.germline.png and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.rawprofile.png b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.rawprofile.png deleted file mode 100644 index 2768b41..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.rawprofile.png and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.samplestatistics.txt b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.samplestatistics.txt deleted file mode 100644 index 5adb9f9..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.samplestatistics.txt +++ /dev/null @@ -1,7 +0,0 @@ -NormalContamination 0.0100800364066352 -Ploidy 1.98395941206446 -rho 0.99 -psi 2 -goodnessOfFit 76.7600171579724 -GenderChr Y -GenderChrFound Y diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.sunrise.png b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.sunrise.png deleted file mode 100644 index d1c673f..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.sunrise.png and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.tumour.png b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.tumour.png deleted file mode 100644 index 6fc9087..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/ascat/COLO-829.tumour.png and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829-BL.brm.bam b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829-BL.brm.bam deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829-BL.brm.bam +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829-BL.brm.bam.bai b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829-BL.brm.bam.bai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829-BL.brm.bam.bai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829.brm.bam b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829.brm.bam deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829.brm.bam +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829.brm.bam.bai b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829.brm.bam.bai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829.brm.bam.bai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.bedpe.gz b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.bedpe.gz deleted file mode 100644 index 07638d0..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.bedpe.gz and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.bedpe.gz.tbi b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.bedpe.gz.tbi deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.bedpe.gz.tbi +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.vcf.gz b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.vcf.gz deleted file mode 100644 index 1ea94b5..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.vcf.gz and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.vcf.gz.tbi b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.vcf.gz.tbi deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.annot.vcf.gz.tbi +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.intermediates.tar.gz b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.intermediates.tar.gz deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.intermediates.tar.gz +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.ngscn.abs_cn.bw b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.ngscn.abs_cn.bw deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/brass/COLO-829_vs_COLO-829-BL.ngscn.abs_cn.bw +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/COLO-829_vs_COLO-829-BL.annot.muts.vcf.gz b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/COLO-829_vs_COLO-829-BL.annot.muts.vcf.gz deleted file mode 100644 index 419f3f8..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/COLO-829_vs_COLO-829-BL.annot.muts.vcf.gz and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/COLO-829_vs_COLO-829-BL.annot.muts.vcf.gz.tbi b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/COLO-829_vs_COLO-829-BL.annot.muts.vcf.gz.tbi deleted file mode 100644 index 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b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/COLO-829_vs_COLO-829-BL.snps.ids.vcf.gz.tbi deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/COLO-829_vs_COLO-829-BL.snps.ids.vcf.gz.tbi +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/alg_bean b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/alg_bean deleted file mode 100644 index 0fb9883..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/alg_bean +++ /dev/null @@ -1,4 +0,0 @@ -rd_pos 2.63;47.37;23.68;13.16;13.16 -base_qual 0-9;10-19;20-24;25-29;30-34;35-39;40-200 -map_qual 0-60;255-255;61-254 -lane 2649_1;2651_1;2653_1;2655_1;2657_1;2660_1;2662_1;2664_1;2666_1;2668_1;2670_1;2672_1;2674_1;2676_1;2678_1;2680_1;2683_1;2686_1;2688_1;2690_1;2692_1;2694_1;2696_1;2698_1;2700_1;2703_1;2705_1;2707_1;2709_1;2712_1;2714_1;2716_1;2718_1;2720_1;2722_1;2724_1;2727_1;2729_1;2731_1;2733_1;2735_1;2737_1;2739_1;2741_1;2743_1;2745_1;2747_1;2749_1;2751_1;2753_1;2755_1;2757_1;2759_1;2762_1;2764_1;2767_1;2769_1;2772_1;2774_1;2776_1;2779_1;2781_1;2783_1;2785_1;2787_1;2790_1;2792_1;2650_0;2652_0;2654_0;2656_0;2658_0;2659_0;2661_0;2663_0;2665_0;2667_0;2669_0;2671_0;2673_0;2675_0;2677_0;2679_0;2681_0;2684_0;2685_0;2687_0;2689_0;2691_0;2693_0;2695_0;2697_0;2699_0;2701_0;2702_0;2704_0;2706_0;2708_0;2710_0;2711_0;2713_0;2715_0;2717_0;2719_0;2721_0;2723_0;2725_0;2726_0;2728_0;2730_0;2732_0;2734_0;2736_0;2738_0;2740_0;2742_0;2744_0;2746_0;2748_0;2750_0;2752_0;2754_0;2756_0;2758_0;2760_0;2761_0;2763_0;2765_0;2766_0;2768_0;2770_0;2771_0;2773_0;2775_0;2777_0;2778_0;2780_0;2782_0;2784_0;2786_0;2788_0;2789_0;2791_0;2793_0;2794_0;2795_0;2796_0;2797_0;2798_0;2799_0;2800_0;2801_0;2802_0;2803_0;2804_0;2805_0;2806_0;2807_0;2808_0;2809_0;76_0;77_0;78_0;81_0;994_0;995_0;996_0;997_0;998_0;999_0 diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/caveman.cfg.ini b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/caveman.cfg.ini deleted file mode 100644 index 7648e75..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/caveman.cfg.ini +++ /dev/null @@ -1,14 +0,0 @@ -CWD=/var/spool/cwl -MUT_BAM=/var/spool/cwl/tmp/COLO-829.bam -NORM_BAM=/var/spool/cwl/tmp/COLO-829-BL.bam -REF_IDX=/var/spool/cwl/reference_files/genome.fa.fai -IGNORE=/var/spool/cwl/reference_files/caveman/HiDepth.tsv -ALG_FILE=/var/spool/cwl/WGS_COLO-829_vs_COLO-829-BL/caveman/tmpCaveman/alg_bean -RESULT_DIR=/var/spool/cwl/WGS_COLO-829_vs_COLO-829-BL/caveman/tmpCaveman/results -SPLIT_FILE=/var/spool/cwl/WGS_COLO-829_vs_COLO-829-BL/caveman/tmpCaveman/splitList -SW=0 -SE=0 -DUP=0 -NORMCN=/var/spool/cwl/tmp/norm.cn.bed -TUMCN=/var/spool/cwl/tmp/tum.cn.bed -VER=1.13.2 diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/cov_arr b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/cov_arr deleted file mode 100644 index ca6115c..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/cov_arr and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/prob_arr b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/prob_arr deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/prob_arr +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/splitList b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/splitList deleted file mode 100644 index 3964394..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/caveman/splitList +++ /dev/null @@ -1,3 +0,0 @@ -21 0 25778640 -21 25778640 38209413 -21 38209413 48129895 diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829-BL.full_gender.tsv b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829-BL.full_gender.tsv deleted file mode 100644 index e9f5f72..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829-BL.full_gender.tsv +++ /dev/null @@ -1,5 +0,0 @@ -#CHR POS Count_A Count_C Count_G Count_T Good_depth GENDER -Y 2934912 0 12 0 0 12 XY -Y 4546684 0 4 0 0 4 XY -Y 4549638 0 0 13 0 13 XY -Y 4550107 0 0 0 2 2 XX diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829-BL.full_genotype.tsv b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829-BL.full_genotype.tsv deleted file mode 100644 index 09f0c05..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829-BL.full_genotype.tsv +++ /dev/null @@ -1,93 +0,0 @@ -#CHR POS Count_A Count_C Count_G Count_T Good_depth GENOTYPE -1 65885569 0 0 23 0 23 GG -1 74941293 42 0 0 0 42 AA -1 84722670 26 27 0 0 53 AC -1 95633977 0 0 18 23 41 GT -1 169676486 0 0 45 0 45 GG -1 171794908 0 0 0 53 53 TT -1 237048500 26 0 25 0 51 AG -1 240492734 26 0 25 0 51 AG -10 83757199 0 0 42 0 42 GG -10 106022789 21 18 0 0 39 AC -10 106039185 19 0 17 0 36 AG -10 117612248 28 0 24 0 52 AG -11 17408630 0 0 0 21 21 TT -11 60878662 1 30 0 1 32 CC -11 122713810 43 0 0 0 43 AA -12 998365 0 0 25 16 41 GT -12 12161541 39 0 0 0 39 AA -12 54466095 21 0 24 0 45 AG -12 103772777 19 0 18 0 37 AG -12 109937534 18 0 18 0 36 AG -13 23732199 0 38 0 0 38 CC -13 47505170 0 0 0 24 24 TT -13 63071787 0 41 0 0 41 CC -13 86230913 22 0 17 0 39 AG -13 110818598 0 0 0 42 42 TT -14 34195326 1 31 0 0 32 CC -14 54123959 0 15 1 21 37 CT -14 85125287 0 0 37 0 37 GG -14 97239216 0 21 0 17 38 CT -15 52027777 0 55 0 0 55 CC -15 79696701 0 40 0 0 40 CC -15 86123988 27 0 19 0 46 AG -15 86124555 17 0 19 0 36 AG -16 9654056 0 31 0 0 31 CC -17 3480447 0 12 0 11 23 CT -17 28731415 41 0 0 0 41 AA -18 8080357 19 22 0 0 41 AC -18 21495483 0 50 0 0 50 CC -18 23877175 0 37 0 0 37 CC -18 60027241 0 0 0 42 42 TT -19 8968549 25 25 0 0 50 AC -19 20741589 48 0 0 0 48 AA -19 31078219 12 0 31 0 43 AG -19 41869392 0 33 0 0 33 CC -19 51315824 0 0 29 0 29 GG -19 57739247 55 0 0 0 55 AA -2 9796791 32 0 0 0 32 AA -2 49189921 0 0 0 53 53 TT -2 68166080 26 0 27 0 53 AG -2 179871172 25 0 20 0 45 AG -2 182543455 0 26 0 0 26 CC -2 211060050 0 0 0 36 36 TT -2 234601669 0 0 20 22 42 GT -20 4312153 0 0 56 0 56 GG -20 23347553 0 28 0 30 58 CT -20 39797465 0 0 0 29 29 TT -20 40884676 0 22 0 36 58 CT -20 52951047 17 0 28 0 45 AG -21 19842577 0 37 0 0 37 CC -21 43718483 0 0 43 0 43 GG -3 59736584 0 46 0 0 46 CC -3 68434603 0 0 48 0 48 GG -3 80549257 24 0 30 0 54 AG -3 117800545 0 0 23 26 49 GT -3 160534225 0 0 31 0 31 GG -3 183818416 0 0 33 0 33 GG -4 38776491 0 0 27 33 60 GT -4 53219120 0 0 1 46 47 TT -4 60833758 24 0 20 0 44 AG -4 78270033 20 0 12 0 32 AG -4 138313566 0 0 47 0 47 GG -5 8828383 0 16 11 0 27 CG -5 16784873 0 0 0 27 27 TT -5 90151589 0 0 67 0 67 GG -5 112364945 0 0 52 0 52 GG -5 129194264 24 0 23 0 47 AG -6 47708431 50 0 0 0 50 AA -6 159425707 0 0 0 48 48 TT -6 165557550 22 0 19 0 41 AG -7 24213356 0 33 0 22 55 CT -7 45932669 18 0 17 0 35 AG -7 90773196 0 0 1 53 54 TT -8 12957475 0 36 0 0 36 CC -8 23060256 0 10 0 11 21 CT -8 31445496 32 0 28 0 60 AG -8 75822851 39 0 0 0 39 AA -8 77819857 37 0 0 0 37 AA -8 130459412 0 18 0 27 45 CT -9 26531692 25 21 0 0 46 AC -9 32516864 46 0 0 0 46 AA -9 78831415 20 1 25 0 46 AG -9 137828650 0 0 42 0 42 GG diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829.full_gender.tsv b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829.full_gender.tsv deleted file mode 100644 index 3cbccdc..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829.full_gender.tsv +++ /dev/null @@ -1,5 +0,0 @@ -#CHR POS Count_A Count_C Count_G Count_T Good_depth GENDER -Y 2934912 0 0 0 0 0 XX -Y 4546684 0 0 0 0 0 XX -Y 4549638 0 0 0 0 0 XX -Y 4550107 0 0 0 0 0 XX diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829.full_genotype.tsv b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829.full_genotype.tsv deleted file mode 100644 index a52f9ba..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829.full_genotype.tsv +++ /dev/null @@ -1,93 +0,0 @@ -#CHR POS Count_A Count_C Count_G Count_T Good_depth GENOTYPE -1 65885569 0 0 21 0 21 GG -1 74941293 37 0 0 0 37 AA -1 84722670 37 14 0 0 51 AC -1 95633977 0 0 0 44 44 TT -1 169676486 0 0 70 0 70 GG -1 171794908 0 0 0 85 85 TT -1 237048500 0 0 59 0 59 GG -1 240492734 0 0 74 0 74 GG -10 83757199 0 0 40 0 40 GG -10 106022789 0 25 0 0 25 CC -10 106039185 13 0 0 0 13 AA -10 117612248 0 0 31 0 31 GG -11 17408630 0 0 0 26 26 TT -11 60878662 0 49 0 0 49 CC -11 122713810 39 0 0 0 39 AA -12 998365 0 0 20 30 50 GT -12 12161541 31 0 0 0 31 AA -12 54466095 21 0 27 0 48 AG -12 103772777 21 0 31 0 52 AG -12 109937534 26 0 11 0 37 AG -13 23732199 0 64 0 0 64 CC -13 47505170 0 0 0 54 54 TT -13 63071787 0 53 0 0 53 CC -13 86230913 28 0 31 0 59 AG -13 110818598 0 1 0 46 47 TT -14 34195326 0 52 0 0 52 CC -14 54123959 0 0 0 39 39 TT -14 85125287 0 0 41 0 41 GG -14 97239216 0 49 0 0 49 CC -15 52027777 0 31 0 0 31 CC -15 79696701 1 32 0 0 33 CC -15 86123988 27 1 32 1 61 AG -15 86124555 29 0 30 0 59 AG -16 9654056 0 40 0 0 40 CC -17 3480447 0 11 0 16 27 CT -17 28731415 51 0 0 0 51 AA -18 8080357 0 46 0 0 46 CC -18 21495483 0 46 0 0 46 CC -18 23877175 0 45 0 0 45 CC -18 60027241 0 0 0 47 47 TT -19 8968549 15 32 0 0 47 AC -19 20741589 57 0 0 0 57 AA -19 31078219 17 0 34 0 51 AG -19 41869392 0 36 0 0 36 CC -19 51315824 0 0 49 0 49 GG -19 57739247 47 0 1 0 48 AA -2 9796791 42 0 0 0 42 AA -2 49189921 0 0 0 59 59 TT -2 68166080 44 0 21 0 65 AG -2 179871172 19 0 35 0 54 AG -2 182543455 0 29 0 0 29 CC -2 211060050 0 0 0 42 42 TT -2 234601669 0 0 43 15 58 GT -20 4312153 0 0 81 1 82 GG -20 23347553 0 28 0 33 61 CT -20 39797465 0 0 1 42 43 TT -20 40884676 0 48 0 40 88 CT -20 52951047 28 0 36 0 64 AG -21 19842577 0 49 0 0 49 CC -21 43718483 0 0 49 0 49 GG -3 59736584 0 55 0 0 55 CC -3 68434603 0 0 74 0 74 GG -3 80549257 51 0 29 0 80 AG -3 117800545 0 0 30 36 66 GT -3 160534225 0 0 67 1 68 GG -3 183818416 0 0 49 0 49 GG -4 38776491 0 0 24 22 46 GT -4 53219120 0 0 0 59 59 TT -4 60833758 33 0 35 0 68 AG -4 78270033 32 0 36 0 68 AG -4 138313566 1 0 69 1 71 GG -5 8828383 0 0 29 0 29 GG -5 16784873 0 0 0 35 35 TT -5 90151589 0 0 49 0 49 GG -5 112364945 0 0 43 0 43 GG -5 129194264 0 0 38 0 38 GG -6 47708431 67 0 0 0 67 AA -6 159425707 0 0 0 49 49 TT -6 165557550 19 0 30 0 49 AG -7 24213356 0 40 0 48 88 CT -7 45932669 33 0 21 0 54 AG -7 90773196 0 0 0 71 71 TT -8 12957475 0 37 0 0 37 CC -8 23060256 1 19 0 21 41 CT -8 31445496 41 0 28 0 69 AG -8 75822851 58 0 0 0 58 AA -8 77819857 63 0 0 0 63 AA -8 130459412 0 28 1 25 54 CT -9 26531692 34 0 0 0 34 AA -9 32516864 72 0 0 0 72 AA -9 78831415 40 0 26 0 66 AG -9 137828650 0 0 49 0 49 GG diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829_vs_COLO-829-BL.genotype.txt b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829_vs_COLO-829-BL.genotype.txt deleted file mode 100644 index dd3f4fe..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/COLO-829_vs_COLO-829-BL.genotype.txt +++ /dev/null @@ -1,10 +0,0 @@ -#GENERAL LOCI -frac_informative_genotype 1 -frac_matched_genotype 0.869565217391304 -genotype COLO-829 GG,AA,AC,TT,GG,TT,GG,GG,GG,CC,AA,GG,TT,CC,AA,GT,AA,AG,AG,AG,CC,TT,CC,AG,TT,CC,TT,GG,CC,CC,CC,AG,AG,CC,CT,AA,CC,CC,CC,TT,AC,AA,AG,CC,GG,AA,AA,TT,AG,AG,CC,TT,GT,GG,CT,TT,CT,AG,CC,GG,CC,GG,AG,GT,GG,GG,GT,TT,AG,AG,GG,GG,TT,GG,GG,GG,AA,TT,AG,CT,AG,TT,CC,CT,AG,AA,AA,CT,AA,AA,AG,GG -genotype COLO-829-BL GG,AA,AC,GT,GG,TT,AG,AG,GG,AC,AG,AG,TT,CC,AA,GT,AA,AG,AG,AG,CC,TT,CC,AG,TT,CC,CT,GG,CT,CC,CC,AG,AG,CC,CT,AA,AC,CC,CC,TT,AC,AA,AG,CC,GG,AA,AA,TT,AG,AG,CC,TT,GT,GG,CT,TT,CT,AG,CC,GG,CC,GG,AG,GT,GG,GG,GT,TT,AG,AG,GG,CG,TT,GG,GG,AG,AA,TT,AG,CT,AG,TT,CC,CT,AG,AA,AA,CT,AC,AA,AG,GG -#GENDER LOCI -frac_match_gender 0.25 -gender XY -gender COLO-829 XX,XX,XX,XX -gender COLO-829-BL XY,XY,XY,XX diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/result.json b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/result.json deleted file mode 100644 index f3a11a6..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/genotyped/result.json +++ /dev/null @@ -1 +0,0 @@ -{"compared_against":"COLO-829-BL","total_loci_gender":4,"tumours":[{"genotype":{"frac_informative_genotype":1,"frac_matched_genotype":0.869565217391304},"gender":{"frac_match_gender":0.25,"gender":"XY"},"sample":"COLO-829"}],"total_loci_genotype":92} diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.annot.vcf.gz b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.annot.vcf.gz deleted file mode 100644 index 48ded7d..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.annot.vcf.gz and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.annot.vcf.gz.tbi b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.annot.vcf.gz.tbi deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.annot.vcf.gz.tbi +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.flagged.vcf.gz b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.flagged.vcf.gz deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.flagged.vcf.gz +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.flagged.vcf.gz.tbi b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.flagged.vcf.gz.tbi deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.flagged.vcf.gz.tbi +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.germline.bed.gz b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.germline.bed.gz deleted file mode 100644 index 2a497e3..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.germline.bed.gz and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.germline.bed.gz.tbi b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.germline.bed.gz.tbi deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL.germline.bed.gz.tbi +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_mt.bam b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_mt.bam deleted file mode 100644 index bd27f3f..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_mt.bam and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_mt.bam.bai b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_mt.bam.bai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_mt.bam.bai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_mt.bam.md5 b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_mt.bam.md5 deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_mt.bam.md5 +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_wt.bam b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_wt.bam deleted file mode 100644 index 86d3acb..0000000 Binary files a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_wt.bam and /dev/null differ diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_wt.bam.bai b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_wt.bam.bai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_wt.bam.bai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_wt.bam.md5 b/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_wt.bam.md5 deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpwgs/bam_bai_pu_pl/WGS_COLO-829_vs_COLO-829-BL/pindel/COLO-829_vs_COLO-829-BL_wt.bam.md5 +++ /dev/null @@ -1 +0,0 @@ - diff --git a/scripts/analysisWGS.sh b/scripts/analysisWGS.sh index 51c264b..14cfc3e 100755 --- a/scripts/analysisWGS.sh +++ b/scripts/analysisWGS.sh @@ -61,7 +61,6 @@ if [ ! -f $PARAM_FILE ]; then exit 1 fi source $PARAM_FILE -env if [ -z ${CPU+x} ]; then CPU=`grep -c ^processor /proc/cpuinfo` @@ -137,7 +136,7 @@ if [ "$ALN_EXTN" == "cram" ]; then ## prime the cache USER_CACHE=$OUTPUT_DIR/ref_cache export REF_CACHE=$USER_CACHE/%2s/%2s/%s - export REF_PATH=$REF_CACHE:http://www.ebi.ac.uk/ena/cram/md5/%s + export REF_PATH=$REF_CACHE do_parallel[cache_POP]="seq_cache_populate.pl -root $USER_CACHE $REF_BASE/genome.fa" fi @@ -164,25 +163,6 @@ do_parallel[CaVEMan_setup]="caveman.pl \ -x $CONTIG_EXCLUDE \ -p setup" -echo -e "\t[Parallel block 1] BB splitlocifiles added..." -if [ ! -z ${SKIPBB+x} ]; then - do_parallel[splitlocifiles]="echo 'BB splitlocifiles count disabled by params'" -else - do_parallel[splitlocifiles]="battenberg.pl \ - -o $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/battenberg \ - -u $REF_BASE/battenberg/1000genomesloci \ - -e $REF_BASE/battenberg/impute/impute_info.txt \ - -c $REF_BASE/battenberg/probloci.txt \ - -r $REF_BASE/genome.fa.fai \ - -ig $REF_BASE/battenberg/ignore_contigs.txt \ - -ge XX \ - -tb $BAM_MT_TMP \ - -nb $BAM_WT_TMP \ - -p splitlocifiles \ - -nl 50 \ - -t $CPU" -fi - if [ ! -z ${SKIPQC+x} ]; then do_parallel[geno]="echo 'Genotype Check disabled by params'" do_parallel[verify_WT]="echo 'VerifyBam Normal disabled by params'" @@ -213,25 +193,6 @@ unset do_parallel declare -A do_parallel echo -e "\nSetting up Parallel block 2" -echo -e "\t[Parallel block 2] BB alleleCount added..." -if [ ! -z ${SKIPBB+x} ]; then - do_parallel[alleleCount]="echo 'BB allele count disabled by params'" -else - do_parallel[alleleCount]="battenberg.pl \ - -o $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/battenberg \ - -u $REF_BASE/battenberg/1000genomesloci \ - -e $REF_BASE/battenberg/impute/impute_info.txt \ - -c $REF_BASE/battenberg/probloci.txt \ - -r $REF_BASE/genome.fa.fai \ - -ig $REF_BASE/battenberg/ignore_contigs.txt \ - -ge XX \ - -tb $BAM_MT_TMP \ - -nb $BAM_WT_TMP \ - -p allelecount \ - -nl 50 \ - -t $CPU" -fi - echo -e "\t[Parallel block 2] CaVEMan split added..." do_parallel[CaVEMan_split]="caveman.pl \ -r $REF_BASE/genome.fa.fai \ @@ -272,6 +233,7 @@ do_parallel[ascat]="ascat.pl \ -r $REF_BASE/genome.fa \ -q 20 \ -g L \ + -l $REF_BASE/gender.tsv \ -rs '$SPECIES' \ -ra $ASSEMBLY \ -pr $PROTOCOL \ @@ -322,6 +284,7 @@ set -x ASCAT_CN="$OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/ascat/$NAME_MT.copynumber.caveman.csv" perl -ne '@F=(split q{,}, $_)[1,2,3,4]; $F[1]-1; print join("\t",@F)."\n";' < $ASCAT_CN > $TMP/norm.cn.bed perl -ne '@F=(split q{,}, $_)[1,2,3,6]; $F[1]-1; print join("\t",@F)."\n";' < $ASCAT_CN > $TMP/tum.cn.bed +NORM_CONTAM=`perl -ne 'if(m/^rho\s(.+)\n/){print 1-$1;}' $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/ascat/$NAME_MT.samplestatistics.txt` set +x # unset and redeclare the parallel array ready for next block @@ -368,7 +331,8 @@ do_parallel[CaVEMan]="caveman.pl \ -e $CAVESPLIT \ -o $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/caveman \ -x $CONTIG_EXCLUDE \ - -no-flagging" + -k $NORM_CONTAM \ + -no-flagging -noclean" echo "Starting Parallel block 4: `date`" run_parallel do_parallel @@ -411,28 +375,34 @@ do_parallel[cgpPindel_annot]="AnnotateVcf.pl -t -c $REF_BASE/vagrent/vagrent.cac -i $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/pindel/${NAME_MT}_vs_${NAME_WT}.flagged.vcf.gz \ -o $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/pindel/${NAME_MT}_vs_${NAME_WT}.annot.vcf" -echo -e "\t[Parallel block 5] cgpFlagCaVEMan added..." -do_parallel[cgpFlagCaVEMan]="cgpFlagCaVEMan.pl \ - -i $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/caveman/${NAME_MT}_vs_${NAME_WT}.muts.ids.vcf.gz \ - -o $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/caveman/${NAME_MT}_vs_${NAME_WT}.flagged.muts.vcf \ - -s '$SPECIES' \ - -m $BAM_MT_TMP \ - -n $BAM_WT_TMP \ +echo -e "\t[Parallel block 5] CaVEMan flag added..." +do_parallel[CaVEMan_flag]="caveman.pl \ + -r $REF_BASE/genome.fa.fai \ + -ig $REF_BASE/caveman/HiDepth.tsv \ -b $REF_BASE/caveman/flagging \ - -g $GERMLINE_BED.gz \ - -umv $REF_BASE/caveman \ -ab $REF_BASE/vagrent \ - -ref $REF_BASE/genome.fa.fai \ + -u $REF_BASE/caveman \ + -s '$SPECIES' \ + -sa $ASSEMBLY \ + -t $CPU \ + -st $PROTOCOL \ + -tc $TMP/tum.cn.bed \ + -nc $TMP/norm.cn.bed \ + -td 5 -nd 2 \ + -tb $BAM_MT_TMP \ + -nb $BAM_WT_TMP \ -c $SNVFLAG \ - -v $REF_BASE/caveman/flagging/flag.to.vcf.convert.ini" + -f $REF_BASE/caveman/flagging/flag.to.vcf.convert.ini \ + -e $CAVESPLIT \ + -o $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/caveman \ + -x $CONTIG_EXCLUDE \ + -k $NORM_CONTAM \ + -in $GERMLINE_BED.gz \ + -p flag" echo "Starting Parallel block 5: `date`" run_parallel do_parallel -# compress and index flagged caveman -bgzip $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/caveman/${NAME_MT}_vs_${NAME_WT}.flagged.muts.vcf -tabix -p vcf $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/caveman/${NAME_MT}_vs_${NAME_WT}.flagged.muts.vcf.gz - # unset and redeclare the parallel array ready for next block unset do_parallel declare -A do_parallel @@ -446,7 +416,7 @@ do_parallel[CaVEMan_annot]="AnnotateVcf.pl -t -c $REF_BASE/vagrent/vagrent.cache -o $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/caveman/${NAME_MT}_vs_${NAME_WT}.annot.muts.vcf" if [ ! -z ${SKIPQC+x} ]; then - do_parallel[verify_WT]="echo 'VerifyBam Tumour disabled by params'" + do_parallel[verify_MT]="echo 'VerifyBam Tumour disabled by params'" else echo -e "\t[Parallel block 6] VerifyBam Tumour added..." do_parallel[verify_MT]="verifyBamHomChk.pl -d 25 \ @@ -464,9 +434,6 @@ run_parallel do_parallel # clean up log files rm -rf $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/*/logs -# cleanup battenberg logs -rm -f $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}/battenberg/tmpBattenberg/logs/* - # correct default filenames from contamination jobs mv $OUTPUT_DIR/timings/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.time.verify_WT $OUTPUT_DIR/timings/${PROTOCOL}_${NAME_WT}.time.verify_WT mv $OUTPUT_DIR/timings/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.time.verify_MT $OUTPUT_DIR/timings/${PROTOCOL}_${NAME_MT}.time.verify_MT @@ -484,7 +451,11 @@ fi echo 'Package results' # timings first tar -C $OUTPUT_DIR -zcf $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.timings.tar.gz timings -tar -C $OUTPUT_DIR -zcf $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.result.tar.gz ${PROTOCOL}_${NAME_MT}_vs_${NAME_WT} ${PROTOCOL}_${NAME_MT} ${PROTOCOL}_${NAME_WT} +if [ ! -z ${SKIPQC+x} ]; then + tar -C $OUTPUT_DIR -zcf $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.result.tar.gz ${PROTOCOL}_${NAME_MT}_vs_${NAME_WT} +else + tar -C $OUTPUT_DIR -zcf $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.result.tar.gz ${PROTOCOL}_${NAME_MT}_vs_${NAME_WT} ${PROTOCOL}_${NAME_MT} ${PROTOCOL}_${NAME_WT} +fi cp $PARAM_FILE $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.run.params echo -e "\nWorkflow end: `date`" diff --git a/scripts/ds-cgpwgs.pl b/scripts/ds-cgpwgs.pl index 96572ba..2d78715 100644 --- a/scripts/ds-cgpwgs.pl +++ b/scripts/ds-cgpwgs.pl @@ -28,7 +28,6 @@ 'a|annot=s' => \$opts{'a'}, 'si|snv_indel=s' => \$opts{'si'}, 'cs|cnv_sv=s' => \$opts{'cs'}, - 'sc|subcl=s' => \$opts{'sc'}, 'qc|qcset=s' => \$opts{'qc'}, 't|tumour=s' => \$opts{'t'}, 'tidx=s' => \$opts{'tidx'}, @@ -37,7 +36,6 @@ 'e|exclude=s' => \$opts{'e'}, 'sp|species:s' => \$opts{'sp'}, 'as|assembly:s' => \$opts{'as'}, - 'sb|skipbb' => \$opts{'sb'}, 'sq|skipqc' => \$opts{'sq'}, 'cr|cavereads:i' => \$opts{'cr'}, 'pc|pindelcpu:i' => \$opts{'pc'}, @@ -96,7 +94,6 @@ && $opts{'r'} eq $opts{'si'} && $opts{'r'} eq $opts{'cs'} && $opts{'r'} eq $opts{'qc'} - && (exists $opts{'sb'} || $opts{'r'} eq $opts{'sc'}) && -d $opts{'r'}) { $ref_area = $opts{'r'}; $ref_unpack = 0; @@ -107,7 +104,6 @@ ref_unpack($ref_area, $opts{'si'}); ref_unpack($ref_area, $opts{'cs'}); ref_unpack($ref_area, $opts{'qc'}); - ref_unpack($ref_area, $opts{'sc'}) if(! exists $opts{'sb'}); } ## now complete the caveman flaging file correctly @@ -115,10 +111,6 @@ my $run_file = $opts{'o'}.'/run.params'; open my $FH,'>',$run_file or die "Failed to write to $run_file: $!"; -# Force explicit checking of file flush -print $FH "export PCAP_THREADED_NO_SCRIPT=1\n"; -print $FH "export PCAP_THREADED_FORCE_SYNC=1\n"; -print $FH "export PCAP_THREADED_LOADBACKOFF=1\n"; print $FH "export PCAP_THREADED_REM_LOGS=1\n"; # hard-coded printf $FH "PROTOCOL=WGS\n"; @@ -268,18 +260,18 @@ sub ref_unpack { =head1 NAME -dh-wrapper.pl - Generate the param file and execute analysisWGS.sh (for dockstore) +ds-cgpwgs.pl - Generate the param file and execute analysisWGS.sh (for dockstore) =head1 SYNOPSIS -dh-wrapper.pl [options] [file(s)...] +ds-cgpwgs.pl [options] [file(s)...] Required parameters: -reference -r Path to core reference tar.gz -annot -a Path to VAGrENT*.tar.gz -snv_indel -si Path to SNV_INDEL*.tar.gz -cnv_sv -cs Path to CNV_SV*.tar.gz - -subcl -sc Path to SUBCL*.tar.gz + -qcset -qc Path to qcGenotype*.tar.gz -tumour -t Tumour [CR|B]AM file -tidx Tumour [CR|B]AM index (bai|csi|crai) -normal -n Normal [CR|B]AM file @@ -290,7 +282,6 @@ =head1 SYNOPSIS Optional parameters -species -sp Species name (may require quoting) -assembly -as Reference assembly - -skipbb -sb Skip Battenberg allele counts -pindelcpu -pc Max CPUs for pindel analysis, >8 ignored [8] -outdir -o Set the output folder [$HOME] -cores -c Set the number of cpu/cores available [default all]. @@ -312,23 +303,29 @@ =head1 OPTION DETAILS =item B<-reference> -Path to mapping tar.gz reference files +Path to mapping tar.gz reference bundle or root of all expanded reference bundles. + +e.g. for each ref bundle needed + +mkdir expanded +curl -L ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/.../core_ref_xxx.tar.gz \ +tar -C expanded --strip-components 1 -zx =item B<-annot> -Path to VAGrENT*.tar.gz +Path to VAGrENT*.tar.gz reference bundle or root of all expanded reference bundles. =item B<-snv_indel> -Path to Path to SNV_INDEL*.tar.gz +Path to SNV_INDEL*.tar.gz reference bundle or root of all expanded reference bundles. =item B<-cnv_sv> -Path to Path to CNV_SV*.tar.gz +Path to CNV_SV*.tar.gz reference bundle or root of all expanded reference bundles. -=item B<-subcl> +=item B<-qcset> -Path to Path to SUBCL*.tar.gz +Path to qcGenotype*.tar.gz reference bundle or root of all expanded reference bundles. =item B<-tumour> @@ -352,10 +349,6 @@ =head1 OPTION DETAILS Specify overriding assembly, by default will select the most prevelant entry in [CR|B]AM header (to cope with inclusion of viral/decoy sequences). -=item B<-skipbb> - -Disables the Battenberg allele count generation - =item B<-skipqc> Disable genotype, gender and verifyBamID. Generally you want to set this for non-human data