How to remove a chr from a bam file?

Question

[mbk0asis]

Hi.

If you want to remove reads mapped on a certain chr, how would you do that?

I know 'samtools' can extract reads on a chr. Extraction of each chr and combining chr data I want would solve the problem, but I have multiple bam files to run it.

So, if anyone of you know how to REMOVE a single chr (e.g. chr1 only), please tell me.

Thank you!

Answer 1

[Ashutosh Pandey]

See this post: Remove mitochondrial reads from BAM files

[mbk0asis]

Thanks! It's the answer I wanted.

[Ram]

I've moved Ashutosh's comment to an answer. Please accept it.