Entering edit mode
11.0 years ago
mikhail.shugay
3.5k
Here is a simple script (based on java/groovy) that does the following things for variant calls:
- Identifies parent gene segment (Exon/Intron/UTR)
- translates related codons (and identifies missense mutations)
- checks if variant is a known SNPs (dbSNP) or cancer-associated mutation (COSMIC)
Download links here: http://100bp.wordpress.com/2013/04/24/vcf-file-annotation/
The only prerequisite is an archive of refgene track (hg19) and latest (as of 2013) dbsnp/cosmic entries which goes with the distribution. Hope this will be useful
