As far as I know, the Broad's Picard team are implementing the UMI in their pipelines using the RX and QX tags for the UMI sequence and base quality.
I do not think that they are trying to set the standard for the whole community but they needed something for their work. I am not in that group, and don't presume to make announcements for them, but I also needed to put them somewhere so I stuck mine there too.
They put the UMIs into their BAMs early on in the process (BCL level). I get the data at a later stage so I have to strip off the UMIs, align, and then put them back into the bam taking them off of the FASTQ file. This is obviously a subpar hack but I have code to support the hack here if you like that standard:
Thank you for raising this issue. I agree this needs a standard so it doesn't turn into the old chr1 vs 1 trap.
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