"PASS" variants Octopus detects also have tons of alternate reads in the normal sample

[Mathieu179]

I’m trying to use octopus to call SNVs and indels in cancer-normal mode.

But all the "PASS" variants Octopus detects (whether or not using the --somatic-only option) also have tons of alternate reads in the normal sample.

I’m using the command line from the GitHub with GH38:

octopus -R Homo_sapiens_assembly38.fa -I normal.bam tumour.bam --normal-sample NORMAL

octopus v0.7.4 (develop 9748f5a)

where "NORMAL" is the SM flag in the read group of my normal bam.

There are no errors during the run. Would you have an idea where this might go wrong?