UMI in Sam Tag

[caleblareau]

I would like to request support for processing UMI data that is contained in a sam tag (e.g. the UB tag in 10x data-- https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/bam). This is supported in Picard. https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.7.0/picard_sam_markduplicates_UmiAwareMarkDuplicatesWithMateCigar.php

I understand the temporary alternative is to modify my read names, but it would be really nice if this could be included as a feature.

[sfchen]

Thanks, this is a good suggestion.

[SPPearce]

Is this likely to happen at any point? I have the UMIs present in a tag, as required by fgbio, and would like to compare. Or is there an easy way to move them from a tag to the read name?