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broadinstitute / picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
https://broadinstitute.github.io/picard/
MIT License
965 stars 367 forks source link

AddOrReplaceReadGroups should support addition of the BC tag #1627

Open arkal opened 3 years ago

arkal commented 3 years ago

Feature request

Tool(s) involved

AddOrReplaceReadGroups

Description

The Sam specification provides support for 14 different tags in the sam Read Group section of the SAM header. Picard supports 13 of these, leaving out the BC tag representing the index sequences used to demultiplex reads assigned to this library. The tag is useful for QC purposes and should be supported by the tool.

kbergin commented 3 years ago

We would definitely want this tool to support that tag, thank you for pointing it out. If you're interested in making a PR to add this support we'd be happy to see one. Otherwise we will add it to the backlog.

arkal commented 3 years ago

I'm not a java programmer so i can wait for you to implement it. Thanks!