Brent Pedersen

yes, I'm open to a PR. please keep me posted. I'm picky about adding features and don't want you to do a bunch of work only to run into my...

From your link, the BQs reported are 2, 9, 24, 40 or 2, 12, 24, 40. Those fall in different bins as defined by fraguracy so the fraguracy conversion is...

That's a large cohort! What is the exitcode when it fails within seconds? I think you might be hitting memory limits. Maybe you can split to smaller groups of e.g....

That cutoff should generally be ok. The problem is if you have 20K samples, and a single sample with low-quality, that may appear to be related at that level to...

Hi Felix, do you mean by pooled that all reads from all samples are mixed, without barcodes so you don't know which reads came from which samples? It's possible that...

hi, it looks like mosdepth has not been updated to v0.3.9 on bioconda and i think quay pulls from there.

Thanks, I'll have a look again. Might just copy a lot of code for simplicity into pbr. Yeah. I'd prefer to use noodles, but obviously there's more overhead to getting...

hi Louis, the coverage part of covstats won't be reliable for cram. for low coverage, you should be able to run [mosdepth](https://github.com/brentp/mosdepth) on cram in a few seconds. it will...

hi, there are other issues on this. It's basically a design mistake that I made when starting out and now am hesitant to change for backward compatibility. If record.FILTER is...

hi, did you use bwa mem via bwa-meth? or bwa-mem2 or other? if you can make a pair of fastqs with just these reads, I could try to have a...