Issue: chr6_PATERNAL:138175962-138175962

[nhansen]

Assembly Region

chr6_PATERNAL:138175962-138175962

Assembly Version

v0.7

DeepVariant Call

chr6_PATERNAL 138175962 chr6_PATERNAL_138175962_T_C T C 46 . AF=0.666667;AQ=46 GT:AD:DP:GQ:PL 1/1:1,19:20:23:39,23,0 0/1:11,15:26:46:46,0,57 0/1:15,11:27:34:34,0,54

[jzook]

Looks like a mis-genotype by Onso in HG002 as homozygous, since for some reason (maybe unlikely random sampling?) only 1/20 onso reads in HG2 supports the ref allele, even though ~50% of reads in Element and HiFi support ref

[fleharty]

I agree with @jzook here. The T->C variant appears to be a misgenotype in HG002 called as HOMVAR, but it is most likely HET. Some additional evidence that it is HET is that the neighboring phased variants (two base insertion and G->C SNP) also appear to be HET.