Unified genotyper- reduced reads issue with indel calling
I find the behaviour of UG with reduced reads and indels very odd. I am using the 2.7.4 GATK and I am dealing with an indel that looks completely legit in the normal BAM:
11 47354522 C 16 .,..+3CAC,+3cac.,,+3cac,+3cac..+3CAC,.,,, :=>!!=>!!>!=?;>>
The reduced BAM mpileup looks like:
11 47354522 C 9 ,,+3cac..+3CAC,.,,, C!>!=?;>>
which I don't really have an issue with. I presume the forward and reverse reads containing the indels were collapsed into two composite reads.
Now this indel absolutely refuses to be called, until I set the option
and then the indel is found and called. It is as if the UG could not see that the reads supporting the indel are collapsed.
Similarly in the VCF file the call looks like:
So depth 10, which I cannot make sense of. In any case with 2 reads supporting the indel, it is not consistent with the unreduced BAM file.
Is there something I do not understand here, or is there a bug with the handling of indels and the GATK UG?
Thank you in advance for suggestions,