I am trying to get the consensus sequence region from a .bam file.
samtools mpileup -C50 -gf ref.fa -r Chr13:1,000-2,000 aln.bam
and I got
[bam_parse_region] fail to determine the sequence name.
[mpileup] malformatted region or wrong seqname for US-18.bam
Please, waht am I doing wrong? I really need to figure out but I have no experience with it