Snps Only In Chromosomes 1-6

Question

[GPR]

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

Answer 1

[JC]

That's not normal. Check your pipeline and filtering options.

Answer 2

[Chris Miller]

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.