double line entries for indels.

[curtisjamison]

Hi Strelka team -

We occassionally see double line entries around indels. The first entry is a reference call for the base before the indel, and the second entry is the actual indel:

chr1 1654065 . A . . HighDepth . GT:GQX:DP:DPF:MIN_DP 0/0:21:8:0:8 chr1 1654065 rs35174499 AGCG A 105.0 PASS CIGAR=1M3D;RU=GCG;REFREP=1;IDREP=0;MQ=45 GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL 1/1:18:11:8:0,7:0,7:0,0:PASS:147,21,0

Have you seen this before?

Thanks, Curt

[ctsa]

Indels use a prefix base, so this is how the caller currently works if there is an adjacent SNV or (in this case), a fragmented gVCF reference block.