Merge bam files for duplicates prior to calling peaks

[sthair]

Hi there, I am wondering if there is a way to merge the _sort_dedup.bam files for duplicate samples, assign to rmdup_bam, and then call peaks/ run the rest of the pipe from that. These are paired end samples FYI thanks! Simone

[nsheff]

is there a reason you want the earlier steps run separately? If not you can use this:

https://pepkit.github.io/docs/sample_subannotation/

it will merge them at the beginning, though.