Best practices to find intersection among variants
"Blanchette, Marco" <[email protected]> Mon, 25 Aug 2014 23:35:30 +0000
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <D0213286.87A5B%[email protected]> |
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 cant 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor