Nils Homer

@dstephensSD you could probably just replace all the bases with As, change the read names to `READ`, and then there's no information left that's a privacy concern. You could also...

@tfenne can you review this when you get the chance? I'd like to fixup based on @sstadick's comments

@yfarjoun thank-you!

@birnbera You're right that `AnnotateBamWithUmis` takes only one FASTQ. Can you try the proposed update in PR #657 where I added support for _multiple_ FASTQs?

@birnbera ~https://github.com/fulcrumgenomics/fgbio/releases/tag/nh_annotate_multiple_fastqs_tag~. Download the JAR there and I can then delete the release.

@birnbera you can also try using `GroupReadsWithUmi -> CallDuplexConsensusReads -> FilterConsensusReads` if you have duplex data versus just using the UMIs to mark duplicates. I'll close this issue once the...

`UmiAwareMarkDuplicatesWithMateCigar` is mainly used to ensure that two or more reads from the same source molecule are not counted twice in downstream variant calling, but why not leverage the multiple...

Agreed unless your always using the thing in Try then it doesn’t make to return a Try. Go for it.

I haven't looked at the Sureselect XT HS technology prep (only the HS2 which is duplex sequencing with dual index sample barcodes). If I recall correctly, the UMI length is...

@eboyden unless @tfenne disagrees (feel free to reopen), we do not to touch that flag as it is completely determined by the aligner (or other upstream tools) and we tend...