Flo

I simply ran `bwa-mem2 index ref.fa` + `bwa-mem2 mem ref.fa r1.fq r2.fq`, same for bwa. @yuk12 Unofrunately i can not share this specific dataset, though i did some experimenting and...

> Is there any chance you could provide a small test case? I am unable to comment without seeing the data unfortunately. Unfortunately I can not share the exact sequences....

Hey, So i can confirm a newly built bcftools is finishing with `--indels-2.0` when run on my original data sets. Though the INDEL calling is still missing the INDELs detected...

I think I managed to create an artificial dataset that reproduces the behaviour as far as i can tell. I took the original mapping and replaced reference sequence and alignments...