[BioC] Best practices to find intersection among variants

Blanchette, Marco MAB at stowers.org
Tue Aug 26 01:35:30 CEST 2014

I am very very new to working with variants, maybe this question is very basic but I need to get kickstarted a bit…

Just ran an analysis to find the common variation in a set of lab strains used in house in the haploid genomes of S. pombe. I used GATK best practices and I am at the stage where I have filtered variants and I would like to find the common ones. My first intuition for this was to turn to R (tired to running Java command line…) and I fumbled on VariantAnnotation which uses my favorite object, GRanges, under the hood. So I should be good.

However, I can’t seem to figure out how to create intersect and I am a bit nervous as I want to find the common variants, not just the location (I can see that I could extract the Granges and do overlap operation on them, but then, I run into the danger of losing the variant information…).

Could anyone provide a simple workflow to get me started? I could provide a basic starting code but it would only be restricted to loading the VariantAnnotation package and reading two vcf files… so I figured that I would not add it…

Thanks a bunch and sorry for the very vcf newby question.

--  Marco Blanchette, Ph.D.
Genomic Scientist
Stowers Institute for Medical Research
1000 East 50th Street
Kansas City MO 64110

Tel: 816-926-4071
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