chr region to bam file

[meghatron21]

Hi. I'm trying to run polysolver on bam files already aligned by someone else.

I'm getting the following error: [bam_parse_region] fail to determine the sequence name. [main_samview] region "6:29941260-29945884" specifies an unknown reference name. Continue anyway. [bam_parse_region] fail to determine the sequence name. [main_samview] region "6:31353872-31357187" specifies an unknown reference name. Continue anyway. [bam_parse_region] fail to determine the sequence name. [main_samview] region "6:31268749-31272105" specifies an unknown reference name. Continue anyway. [samopen] SAM header is present: 194 sequences. [sam_read1] reference 'SN:chrUn_GL000218v1 LN:161147

Which I'm guessing is arising from the bam files having the "chr" prefix and the region being extracted not. Is there a setting to deal with this? I know it was aligned to hg38 for sure.

[Nitin123-4]

bam file has chr and it is looking for (6:29941260-29945884) so open /home/polysolver/scripts/shell_call_hla_type file and add chr (chr6:29941260-29945884) and then run it. Do the same thing for 6:31353872-31357187 and 6:31268749-31272105 and it will work.