Christopher Schröder

Releases

1

This is just a kind request, rather then an issue. It would be highly highly appreciated, if you would create a new official release as soon as the master branch...

Range violation

19

Hello, I have a rather difficult problem. I am aligning several wgs samples, each about 100gb filesize, and for one of them bwa-mem2 avx just stops at 17gb without any...

feat: BWA mem2 index - remove prefix parameter and determine prefix from output

2

### Description Remove the param prefix and detect prefix by output ### QC For all wrappers added by this PR, I made sure that * [x] there is a test...

feat: more informative file names

1

rename reference from "genome.fasta" to genome.{datatype}.{species}.{build}.{release}.fasta rename sample.sorted.bam to sample.bam

Adjust get_read_group for multi sample config.

3

I have projects where I have to use the same sample in multiple groups. For example I have a lot of single case samples, but the parents are sequenced chunkwise...

Gridss

5

This implements my gridss calling pipeline, which is suppose to replace delly as the structural variant caller. Gridss only calls breakends and varlociraptor does not support breakends yet. I suggest...

Missing Reads

2

Dear bazam team: I have noticed that bazam does not output all read pairs. That was quite unexpected for me. Does it have a built-in filter? For example for duplicates?...

Regarding to the description of the AC format field "Allelic depths for the ref and alt alleles in the order listed. [...]" and regarding to the vcf specification "If the...

fix: name of bamqc

6

### Description The subcommand name was wrong in the description. Additionally add a region param fro target analyse. ### QC * [x] I confirm that: For all wrappers added by...

L.start <= R.start

3

Hey, I get the following error for one of my samples in one of my projects ``` strling version: 0.5.1 using first reads in fragment_length_distribution calculation as there were not...