sangtaekim
commented
5 years ago Strelka does not call LOH events. In this example, it is reported as a possible somatic event (with score 0) because the allele frequency is different for normal and tumor samples. The SGT field is provided simply as a "reference" and we don't recommend to use this field to infer genotypes of either sample. Also, Strelka's somatic calls where NT != ref is not reliable and we report them always with score 0.
Thus, an answer to your question is that Strelka's somatic caller doesn't provide a way to distinguish them.
I run strelka2 version 2.9.10 with paired normal-tumor somatic mode, and got an site which indicated that it should be LOH type.
1 241663871 . G A . LowEVS SOMATIC;QSS=30;TQSS=2;NT=het;QSS_NT=30;TQSS_NT=2;SGT=AG->GG;DP=296;MQ=59.12;MQ0=0;ReadPosRankSum=-1.18;SNVSB=0.00;SomaticEVS=0.00;EVSF=0,1,0.5,59.117,0,0,-1.1758,-1.3024,0,0.017964,24,63,0,0 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 116:0:0:0:50,51:0,0:66,66:0,0 167:3:0:0:121,129:0,0:43,49:0,0
However, when I run with paired normal-tumor germline mode, I got the result which indicated it seemed just a germline variant.
1 241663871 . G A 1392 PASS SNVHPOL=2;MQ=59 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:325:292:114:2:65,49:23,16:42,33:-27.0:PASS:326,0,370 0/1:155:155:164:3:43,121:21,53:22,68:-99.0:PASS:370,0,152
So, how to distinguish LOH and germline variants ？
Thank you.