How to change a BAM file so the chromosome identifier is "chr 1" not just "1"

Question

[bruss]

Hi

I'm trying to set up some files to call Super Enhancers using ROSE. I think I have everything I need, however my BAM files may not be formatted properly. using samtools idxstats I realized that the BAM file I'm using lists chromosomes with their numbers (IE: "1") rather than a "chr 1" format which is needed for ROSE. Any idea how I can convert this BAM file to change the chr identifiers? Thanks for any help you can provide!

Answer 1

[GenoMax]

Use samtools reheader:

reheader

    samtools reheader <in.header.sam> <in.bam>

    Replace the header in in.bam with the header in in.header.sam. This command is much faster than replacing the header with a BAM→SAM→BAM conversion.

[Devon Ryan]

For those reading this and wondering, "but what about the chromosome names for each read?!?", the answer is that those names aren't actually stored in a BAM file. Rather, alignments have chromosome index number associated with them and the name you see when you use samtools view is taken from the header.

[bruss]

This worked great, thanks!!