I have used UnifiedGenotyper to call SNPS. I found some SNPs that has been reported from low quality reads in chromosome X and chromosome Y. Is it possible not to take low quality reads into account while calling SNPs using UnifiedGenotyper? Or, do I need to do quality filtering of BAM files before hand ?
I was wondering, in the vcf output from UnifiedGenotyper what metrics go into the variant quality score, QUAL ?
I'm assuming that depth, DP is one of them but I can't find further information. Apologies if I've missed it.
Attached are some plots of the depth and quality distribution for variant calls, and also of the relationship between depth and quality. I'm slightly worried that the bimodal quality distribution indicates an error, otherwise I've just attached the graphs for general interest.
