changing chromosome notation in .BAM file

[ffinkernagel]

You are mistaken. The reads only contain a number that tells which entry from the header to pick.

[ddaneels]

That would be a way to change the header, but if I'm not mistaking the chromosome numbers are also in the actual read-part of the file. So how to change them there?

[dpryan]

Look at the samtools reheader command. Presumably you would just "samtools view -H file.bam > header.sam", edit the header, and then use that with reheader.

[ddaneels]

This is of course one option ... I'm remapping my data for the moment, but since I have 5 .bam files from exome data, it takes quite some time. So I was looking for a faster option

[adaptivegenome]

I think it might be easiest to change the reference fasta file you are using to match the BAM?

[ddaneels]

Hi everyone,

I have .bam files in which the chromosomes are notated as '1', '2', '3', ... 'X', 'Y'.
However, for further analyses I need a .bam file in which the chromosomes are notated as 'chr1', 'chr2', 'chr3', ... 'chrX'. Does someone know a way to do this?

I thought I might need the substitute (s) command ...