Nils Homer

@esamorodnitsky we've used both `CallOverlappingConsensusBases` and `ClipBam` with `--clip-overlapping-reads` (and `--clip-bases-past-mate` potentially). It is really a case by case basis, and I don't think we are ready to add them...

Somehow the `/A` is getting lost between the uBAM and the mapped BAM. I see your filename has `picard` in it, but we don't use `picard` in the best-practices pipeline....

@teryyoung let me know if you still have this problem

This feature was added here: https://github.com/fulcrumgenomics/fgbio/pull/805. The goal was to have a tool that would take individual raw read pairs and if the read and its mate overlap, modify (consensus...

@kcibul feel free to reopen if I didn't answer this question!

@bkohrn wouldn't be too hard to change this line to take in multiple lengths: https://github.com/fulcrumgenomics/fgbio/blob/5aded50627e5b7a893a74e8e3d6a89626226b641/src/main/scala/com/fulcrumgenomics/fastq/TrimFastq.scala#L49, then propagate that further.

What's the objection to just using `FastqToBam` instead of `TrimFastq`?

I'd just pipe into `samtools fastq` like you're doing to be honest. Of course there's no need to use output compression, so set `fgbio --compression 0 FastqToBam. ... | samtools...

Feel free to reopen if this is still an issue.

Please try not adding a read group to the mapped BAM (i.e. don't use `-R` for `bwa mem` to get it working for now. ZipperBams is relatively new and simple,...