Strelka2, problematic GT field. GT:1

Illumina / strelka

Strelka2 germline and somatic small variant caller

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Open iranmdl opened 4 years ago

iranmdl commented 4 years ago

Hello! I have noticed for the first time that sometimes Strelka2 gives to GT field a value of 1. See the following VCF record:

chr1 5553 . A G 78 LowGQX SNVHPOL=3;MQ=40 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 1:428:1:28:2:0,28:0,8:0,20:-34.4:LowGQX:370,0

Is this an expected behaviour? Thank you in advance, Irantzu

neuromol commented 4 years ago

Hey guys any update on this we have the same issue ?

ntm commented 3 years ago

Hi, I've seen these, AFAICR they represent hemizygous calls and occur when the position is overlapped by a heterozygous deletion. I just fix them to homozygous 1/1 calls: https://github.com/ntm/grexome-TIMC-Secondary/blob/0c18e1b79ac2bc3465e3f891bbdc832524ccee15/1_filterBadCalls.pl#L680-L682