Nils Homer

See: https://github.com/samtools/samtools/pull/2287

@msto want to give https://github.com/fulcrumgenomics/fgbio/pull/964 a go?

It may be the case you have extremely high coverage of each template and/or genomic coordinate? Can you check if you have provided enough memory by looking at the memory...

It definitely looks like you have high coverage in that region, which makes it tough. Not knowing your UMI length(s), you may have very high per-molecule coverage. It's not too...

> Found two records that are paired, not supplementary, and first of the pair: NB552094:195:HGLLGBGXH:1:11101:10001 Can you examine at the read pair with this name, and see where the primary...

Since you used `-x`, it makes me even more suspicious about a primary alignment getting lost. Please feel free to re-open if you have more info on this issue.

@Kuanhao-Chao feel free to re-open if you still want this reviewed, and before doing so, please make sure all the tests are passing!

@d-cameron I took a look at what current duplicate marking software does (see below). Nonetheless, I'd like a solution that's not bespoke to solve this issue, since I would like...

@whitwham > It does nothing of the sort. My apologies for mis-interpreting samtools `markdup`, since I read places in the code that filter out supplementary/secondary, but that's just for temporary...

@roryk we're discussing this internally, so that you don't think we have forgotten!