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AIM_trio.sh
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# Merge gVCFs using GLnexus
docker run --rm -i -v $(pwd):/in ghcr.io/dnanexus-rnd/glnexus:v1.4.1 \
bash -c 'glnexus_cli --config DeepVariant /in/*.g.vcf.gz' > S185_186_187_trio.bcf
bcftools view S185_186_187_trio.bcf | bgzip -@ 4 -c > S185_186_187_trio.vcf.gz
#run aim trio
## use hg38 reference : /home/zhijiany/work_dir/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
bash /home/zhijiany/trio_pipeline/trio_pipeline/proc_trio_hg38.sh \
/home/zhijiany/work_dir/06202024/input/VCFs/S185_186_187_trio.vcf.gz \
/home/zhijiany/work_dir/06202024/input/HPO/BCM427_HPO.txt \
trio185 \
/home/zhijiany/trio_pipeline/trio_pipeline \
/home/sasidhar/1023 \
/home/zhijiany/work_dir/06202024/output \
/home/zhijiany/work_dir/06202024/input/trio.ped \
1216620_S185 \
1216621_S186 \
1216622_S187 \
/home/zhijiany/trio_pipeline/trio_pipeline/proc.sh \
hg38 > /home/zhijiany/work_dir/06202024/full_logs.txt 2>&1
#for the vini case
bash /home/zhijiany/trio_pipeline/trio_pipeline/proc_trio_hg38.sh \
/home/zhijiany/work_dir/06242024/input/merged.vcf.gz \
/home/zhijiany/work_dir/06242024/input/hpos.txt \
trio_vini \
/home/zhijiany/trio_pipeline/trio_pipeline \
/home/sasidhar/1023 \
/home/zhijiany/work_dir/06242024/output \
/home/zhijiany/work_dir/06242024/input/pedigree.ped \
2400125487.targeted \
2400125488.targeted \
2400125489.targeted \
/home/zhijiany/trio_pipeline/trio_pipeline/proc.sh \
hg38 > /home/zhijiany/work_dir/06242024/full_logs.txt 2>&1
#build docker from local image
##
cd /mnt/belinda_local/cole/home/trio_pipeline/fixed_singleton_pipeline/AI_MARRVEL/
docker build -t cole/aim-lite:latest .