i'm trying to run intersectBed with a VCF file (produced by complete genomics, version vcf4.1) and a Bed file of the RefSeq genes(downloaded from UCSC table browser), but i don't get any results,
i do know about certains variants included in my list that should appear in the intersection.
i changed the first colomn of the VCF file from "1,2,3...X,Y" to "chr1. chr2... chrX, chrY" (even though i did not see any need for that in the documentation).
my command is :
intersectBed -wa -a RefSeqGenes.bed -b myfile.vcf
strangely, when i run this with a minifile that contains only a few lines (with variants that i expect to be intersected) it works. but when i run it, with a larger vcf file (that contains the whole genome, or even a single chromosome's variants) i get nothing.
any idea why??
your help will be very appreciated :-)))
Moran
i do know about certains variants included in my list that should appear in the intersection.
i changed the first colomn of the VCF file from "1,2,3...X,Y" to "chr1. chr2... chrX, chrY" (even though i did not see any need for that in the documentation).
my command is :
intersectBed -wa -a RefSeqGenes.bed -b myfile.vcf
strangely, when i run this with a minifile that contains only a few lines (with variants that i expect to be intersected) it works. but when i run it, with a larger vcf file (that contains the whole genome, or even a single chromosome's variants) i get nothing.
any idea why??
your help will be very appreciated :-)))
Moran
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