Try SNP See out: http://bioinformaticslab.ucsd.edu/~dmuller/SNP_Feature_View/
SNP See aims to provide the layman and researcher with a free tool for learning about sequence data by highlighting SNP-determined genetic traits from inputted genomic files (VCF and similar)
Read a paper motivating the project here
Built with Django 1.6.5
PyVCF for parsing VCF files. PyVCF can be installed with: pip install pyvcf
Biopython: sudo apt-get install python-biopython
We used JBrowse 1.11.4 in this project: http://jbrowse.org/
We've uploaded a tar ball with the complete JBrowse 1.11.4 directory we used for the project (formatted with reference tracks, and our custom 'SNP See Data' track): https://drive.google.com/file/d/0B_Z3ZgWqIL8nRXUxVy00LXZBOHc/edit?usp=sharing
The JBrowse 1.11.4 folder normally lives in the 'static' folder in the root directory of this repository (next to Bootstrap, and JQuery).
We seeded JBrowse with the (1) GRCh37 human reference sequece, (2) RefSeq genes, and (3) Common SNPs(138). We've uploaded the source data for those 3 tracks for convenience (fasta files for the reference genomes, BED files for the RefSeq genes and Common SNPs(138)): https://drive.google.com/folderview?id=0B_Z3ZgWqIL8nQld0ZjE4WTRQLW8&usp=sharing
All data was originally downloaded from UCSC--we used the table browser for the RefSeq Genes and Common SNPs(138): http://genome.ucsc.edu/cgi-bin/hgTables?org=human
The source tracks were formatted for use in JBrowse, with JBrowse's bin/prepare-refseqs.pl (for the GRCh37 reference sequence), and bin/flatfile-to-json.pl for the RefSeq genes and common SNPs.
Our configuration for the 'SNP See Data' track, contains a bit of custom JavaScript for click actions, so we'll write out the track configuration below. Note that, currently, the action loads a page on our development server ('127.0.0.1:8000/SNP_Feature_View...'). Be sure to change this an appropriate URL if you choose to reuse this code.
"style" : {
"className" : "feature",
"arrowheadClass" : "null"
},
"key" : "SNP See Data",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : null,
"urlTemplate" : "tracks/SNPSee/{refseq}/trackData.json",
"compress" : 0,
"type" : "FeatureTrack",
"label" : "SNPSee",
"onClick" : {
"action" : "function(track, feature, div) { var $ = window.parent.$, jQuery = window.parent.jQuery; var MyData = {}; MyData.name = this.feature.get('name'); $( document ).ready(function() { $( '#feature_view' ).load('http://127.0.0.1:8000/SNP_Feature_View/feature_view/visual_browser/' + MyData.name + '/'); }); }"
All of the genetic information we used as sample genetic files were downloaded from the personal genome project: https://my.pgp-hms.org/public_genetic_data
The sample genetic files we use normally reside in the 'media' folder at the root level of the repository. The 'media' folder was not committed to GitHub (it's large), but is hosted here: https://drive.google.com/folderview?id=0B_Z3ZgWqIL8nMVNHdjhLcmZ6WFk&usp=sharing
The sample genetic files are in media/SNP_Feature_View/sample_files
We've written 2 management scripts: generate_session_data, and create_SNP_BED_file
generate_session_data is invoked with Django as follows: python manage.py generate_session_data
It takes all sample files contained in the Django backing database and searches them for SNP calls that SNP See uses to determine traits. SNP calls contained in the sample file, and used by SNP See, are added to a dictionary and pickled out to a file in media/SNP_Feature_View/sample_files_as_session_data
create_SNP_BED_file is invoked with Django as follows: python create_SNP_BED_file
It takes the SNP relation maintained by Django, and writes it to a BED file--specifically it writes the file media/SNP_Feature_View/JBrowse/BED_files/SNP_BED_file.bed (That BED file can be incorporated into JBrowse for viewing using JBrowse's bin/flatfile-to-json.pl script.)