Felix Lenner
Felix Lenner
#### Is your feature request related to a problem? Please specify. Hi, If I take an aligned BAM, run `samtools reset | samtools fastq -T \*` to get a fastq-file,...
If secondary alignments are filtered out without `--ubam` they should also be filtered out with `--ubam`. Unaligned reads should never have any soft clipped bases, and since `softclipped_bases(&read)` should always...
> The --ubam flag will provide metrics for all reads in the file, regardless of whether they are aligned or not When running with `--ubam` on a file with aligned...
Mimic the behaviour of `nextflow run -r` and allow selected commit(s) to be downloaded. https://nfcore.slack.com/archives/CE5LG7WMB/p1712143905189639 Not sure about the effect it will have on Tower downloads. ## PR checklist -...
### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...
**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md**: **Describe the issue:** When I check the version of google/deepvariant:1.6.1 it says 1.6.0, and the docker image has `ENV VERSION=1.6.0` ``` docker run google/deepvariant:1.6.1...
### Is your feature request related to a problem? Please describe Add a name collision warning for stranger. ### Describe the solution you'd like _No response_ ### Describe alternatives you've...
### Description of the bug Adding this as a reminder that filter_vep can't filter on HGNC_ID in hg38, so I think no clinical set will be generated. Should be [fixed](https://github.com/Ensembl/ensembl-vep/issues/1723)...
### This PR adds | fixes: - Adds STRdust **How to prepare for test**: - [ ] `ssh` to ... - [ ] Install on stage: `bash servers/resources/SERVER.scilifelab.se/update-[THIS_TOOL]-stage.sh [THIS-BRANCH-NAME]` ###...
Hi Brent, I'm having trouble inferring sex after 7740a33. It should be a high quality sample but `n_hom_alt / n_het ~ 0.83`, and sex is therefore not updated I think....