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OpenGene / gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
MIT License
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UMI in Sam Tag #8

Open caleblareau opened 5 years ago

caleblareau commented 5 years ago

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 commented 5 years ago

Thanks, this is a good suggestion.

SPPearce commented 3 years ago

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?