running an application chromosome by chromosome

Question

[Bogdan]

Dear all,

Please could you advise where could I find some TEMPLATE CODE that will allow running MUTECT (or any other program) on each BAM file associated with each chromosome (or chromosome fragment), instead of running it on a BAM file for all chromosomes ;)?

Thanks,

bogdan

Answer 1

[Sam]

If I understand correctly you're essentially trying to split 1 BAM file into several BAM files by chromosome? This can be pretty easily done by using the bamtools -split function as referenced in this topic: How To Split A Bam File By Chromosome

This code will generate individual BAM files for all the chromosomes.

bamtools split -in file.bam -reference

These BAM files can then be fed into your program of choice.