Friederike Hanssen

Can't convert to gistic marker due to input validation

3

Hi, thank you for providing cnvkit and also funcitons to make the ouput compatible for gistic. It is really great to have that. I ran the seg command just fine...

### Name of the tool picard liftover ### Tool homepage https://gatk.broadinstitute.org/hc/en-us/articles/13832753098907-LiftoverVcf-Picard- ### Tool description The tool lifts variants over to different genome version. ### Tool output I haven't found a...

hi, thank you for this fantastic package. I have been playing around with the upset plot function to plot various GenomicRanges objects. I would like to stack my various upset...

Minor: empty output folder for fastp created (see aws ful size tests)

2

### Description of the bug In the full size tests an empty output folder for fastp is created, but no reads are published. Seems to be mostly a cosmetic issue....

Update docs: Haplotypecaller is fine without BQSR (got nothing to do with dragmap)

1

### Description of the bug I just found this forum entry, saying the reason why BQSR was dropped from the DRAGEN-GATK workflow was changes to Haplotypecaller and the addition of...

mixing tumor-only and paired samples and having a tool that only works for paired samples causes the pipeline to fail

3

### Description of the bug When specifying mixed samples (tumor-only and paired) and some tools do not work for tumor-only, like msisensorpro, the pipeline will fail. Reported by @MolPath-Bioinfo on...

### Description of feature Basically add this as a module. I am unclear on the details and what we woud need, but this or something similar would be really great...

Improve CNVKit

3

### Description of feature CNVKit can take sex information: https://github.com/etal/cnvkit/blob/b218280edb266788ea8326596d4283183ce425ea/doc/sex.rst as well as SNP information to to infer b-allel frequency: https://cnvkit.readthedocs.io/en/stable/pipeline.html#snp-allele-frequencies. Adding sex should be simple we track that already...

### Description of feature SnpEff for cancer samples should be run with `-cancer` flag: https://pcingola.github.io/SnpEff/se_cansersamples/ For this we need to add meta data back in as well as tracking the...

Add samtools markdup as duplicate marking alternative

15

### Description of feature With the new template sort Samtools markdup is supposedly much faster than GATK Markduplicates while having similar results. I think this would be worth to add...