provide an example of pipping sambamba in documentation

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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provide an example of pipping sambamba in documentation #504

Closed DrRLS closed 11 months ago

DrRLS commented 1 year ago

I enjoy using Sambamba to in my processing pipeline. I am trying to pipe different commands to create a one liner to process SAM as input and get a sorted BAM file with marked duplicates if possible. This would avoid all the intermediate files generated without pipping.

Can some provide some pointer on how to use sambamba to pipe the following tools, starting with a sam file and ending up with a sorted.dedup.bam? sambamba view > sambamba sort > sambamba markdup

pjotrp commented 11 months ago

There are some options in the docs.