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Marco Blanchette
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220
@marco-blanchette-5439
Last seen 10.1 years ago
United States/Kansas City/Stowers Instiā¦
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
Cell: 816-726-8419
Fax: 816-926-2018
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