No calls from Isaac Variant Caller

Question

[win]

Hi all,

I am analyzing BAMs using Isaac Variant Caller, the resulting VCF has rows where the genotype is 0/0, 0/1,1/0 and 0/0. All such rows have a flag PASS which indicates the data is accurate.

I am interested in finding out genomic locations where there are no calls. Is it accurate to assume that is a row does not have a PASS flag it could be considered as a no call.

Thanks in advance.

Answer 1

[lmainzer]

Hi, Ashkot!

I think that the PASS flag simply indicates that the variant passed the filter criteria set by the iSAAC variant caller. Whether those criteria are satisfactory, the user must decide for himself.

The loci with no variants at all will be marked with a "." in the ALT column, in the output gvcf produced by iSAAC.

Hope this helps,

Luda