I am trying to run samtools on Linux to process BAM files from the
high-coverage sequencing of the Denisovan genome.
When I run mpileup, I get a failed assertion very quickly.
$ time samtools mpileup -C50 -uf human_g1k_v37.fasta T_hg19_1000g.bam
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
samtools: bam_plcmd.c:162: group_smpl: Assertion `q' failed.
Can someone help me with what I am doing wrong, or what is the cause
of the failed assertion?
Thank you very much,
The BAM file I am using can be found at
The alignment FASTA file I am using can be found at