I'm trying to run to get variants called from a (merged) bam file (presumably using bfctools).
$ samtools mpileup merged.bamfile.bam
works fine, spitting out in pileup format.
$ samtools mpileup -g merged.bamfile.bam
I get the following error message
[mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 Assertion failed: (q), function group_smpl, file bam_plcmd.c, line 287. Abort trap: 6
The same thing happens with -u or -v flags.
This is not a general problem, as I can use the flags on a different bam file.