search

marbl / HG002-issues

HG002 human reference genome issue tracking and polishing
10 stars 0 forks source link

Issue: chr17_MATERNAL:74731577-74731577 #643

Closed nhansen closed 1 year ago

nhansen commented 1 year ago

Assembly Region

chr17_MATERNAL:74731577-74731577

Assembly Version

v0.7

DeepVariant Call

chr17_MATERNAL 74731577 chr17_MATERNAL_74731577_T_C T C 62 . AF=0.833333;AQ=62 GT:AD:DP:GQ:PL 1/1:0,8:8:22:36,22,0 1/1:0,23:24:54:62,54,0 0/1:7,14:21:52:59,0,52

fleharty commented 1 year ago

HG002: Onso supports HOM T->C, Element supports HET T->C and ref. HG003: Onso supports HOM T->C HG004: Onso supports HET T->C and ref

Based on the Onso data alone I would call this variant, but the element data shows that HG002 is clearly HET and not HOMVAR.

This indicates that it is possible that this is a correct call, but we really can't know, so I think it is probably better to label this as a False positive.