Flo

Running bcftools mpileup --indels-2.0 fails in combination with --no-reference

1

Either option without the other specified finished successfully, but in combination results in: ``` $ bcftools mpileup -B --no-reference -d 200000 -L 200000 --indels-2.0 -o noref.mpileup.vcf anon_slice.sam [mpileup] 1 samples...

bcftools v1.17 no longer finds known variants from v1.8

14

Hi all, I inherited a setup that uses bcftools 1.8 for variant calling and decided to update to v1.17, but can no longer reproduce the (known) INDEL calls for some...

bwa-mem2 produces different alignment coordinates than original bwa mem

5

Hi, i am currently trying to figure out why my bwa-mem2 version 2.2.1 produces different (and pretty obviously bad) alignments from bwa mem (0.7.18). I run both tools with -K...