Snps Only In Chromosomes 1-6
So I finished a first round SNP identification using samtoools mpileup > varscan > bedtools intersect. My final vcf file contains SNPs only in chromosomes 1-6 and nothing else. Is this normal? Thanks
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Chris Miller
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No, that's not normal. My guess is that one of your steps failed partway through and only processed the first portion of the genome. Check your err logs.
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