[BioC] Best practices to find intersection among variants

[Julian Gehring]

Hi Marco,

Essentially, you want to find a intersection with both the locus and the 
ref/alt alleles matching.  The 'VariantAnnotation' has the 'match' 
function which does this (matching the alt allele).  Here is some of my 
code for getting the common variants from two 'VRanges' objects:

   intersectVRanges <- function(x, y) {
       m = match(x, y)
       s1 = x[!is.na(m)]
       s2 = y[m[!is.na(m)]]
       res = list(s1, s2)
       return(res)
   }

Best
Julian


On 25.08.2014 16:35, Blanchette, Marco wrote:
> 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
> www.stowers.org
>
> Tel: 816-926-4071
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> Fax: 816-926-2018
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