Nils Homer

0. Please let us know how the usage (`fgbio AnnotateBamWithUmis --help`) could be improved. 1. If the FASTQ reads are in the same order as the BAM, then use the...

My apologies for a delay in response as I wont have time in the near future to look at this.

Take a look at the documentation for [`UmiCorrectionMetrics`](http://fulcrumgenomics.github.io/fgbio/metrics/latest/#umicorrectionmetrics). The `umi` column says: > The corrected UMI sequence (or all Ns for unmatched). So the all Ns is for all reads...

I frequently use it, to retrieve the reference sequence, using mainly Java (htsjdk), Python (pysam), and Scala (fgbio) APIs. I find it very useful to not have to have a...

I am using `--alpha 0.0 --alpha 0.5 --alpha 1.0` for two sample mixture.

Perhaps the `--alpha 1.0` is the issue, as it's allowing a "doublet" with 100% one of the samples?

The current behavior is that any read will be counted towards the reference allele.

Excellent! I think the main issue is that it is comparing the first base in the allele, versus the full allele from the VCF and the bases starting at the...

@pditommaso how can I help contribute a PR for this? Is there a good place in the code to start looking?

I should circle back to this. Keeping it open.