do you support aggregation and dedup in one command?

biod / sambamba

Tools for working with SAM/BAM data

http://thebird.nl/blog/D_Dragon.html

GNU General Public License v2.0

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Closed AlisaGU closed 3 years ago

AlisaGU commented 3 years ago

Hi, sambamba is really quick, thanks for your efforts. But, I don't know if it supports aggregation and dedup in one command like this: Merge read groups and mark duplicates per sample (aggregation + dedup).

Can I just pass the multiple inputs belonging to one sample to sambamba in a single command to merge and deduplicate them?

pjotrp commented 3 years ago

Nope.

AlisaGU commented 3 years ago

Thanks for your reply. What should I do to achieve this? use sambamba-merge to merge and sambamba-markdup to dedup?

AlisaGU commented 3 years ago

Hi, Do you agree with my idea?