Entering edit mode
9 months ago
MH85
▴
10
In my vcf file, the sum of total allelic depth (AD) is about half of the raw read depth (DP) for all SNPs. Is it common? If not, any thoughts on what might be the reason(s) behind this?
I use a common pipeline
bwa mem
bcftools mpileup -Ov -Q 20 -R target.txt | bcftools call -mv -Ov
The issue remains even if I generate vcf directly from mpileup and sum allelic depth of all alleles not only reference and alternative.
Thanks a lot in advance