Abra2-processed bams are incompatible with Strelka2

[lculibrk]

Hi there,

I've encountered this recently while trying to run ABRA2-processed bams through Strelka2. Strelka2 appears to yield empty VCFs, with all variants labeled as 'non-candidate' when given ABRA2 bams.

The ABRA2 paper states that "Strelka2 (version 2.9.2)" was used, so there is probably some config options to be fiddled with to fix this. It was encouraging to see what appeared to be config options In https://github.com/mozack/abra2/blob/master/paper/paper.txt however this appears to be for the ABRA1 analysis using Strelka 1.0.x, not ABRA2 using Strelka 2.9.2, as the listed configuration options no longer exist in the Strelka2 binaries, and neither are they mentioned in the tool's source code anymore.

What are the options necessary to run Strelka2 on ABRA2-processed bams ie. to reproduce the analyses in the ABRA2 paper?