-
The package works by putting different input files into a list and processing them one at a time. This is very time-consuming if a user is processing cutaneous sqaumous cell carcninoma whole genome se…
-
Leaving this reminder to myself,
In the workflows I've run I've encountered multiple cases where two SNPs are annotated separately however, in reality, they are DNPs and therefore should have diff…
-
I'm trying to run somaticseq_parallel on some samples VCFs to call the AI consensus.
The version for SomaticSeq is SomaticSeq v3.7.3. Version of XGBOOST is 2.0.2
I've run all mutation callers, then,…
-
Issue by @MaxUlysse, moved from SciLifeLab#666
- [ ] [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) for estimating repeat sizes
- [ ] [QDNAseq](https://github.com/ccagc/QDNAseq) CN…
-
Claire uploaded some VCFs of type we haven't seen before
https://rollbar.com/jimmy.andrews/VariantGrid/items/2457/?utm_campaign=occurrence_message&utm_medium=slack&utm_source=rollbar-notification
```…
-
Hello CNVkit team
I wonder if you advise on the specification of VCF format for the Theta export command:
`cnvkit.py export theta Sample_Tumor.cns reference.cnn -v Sample_Paired.vcf
`
What infor…
-
**Describe the bug**
After recompiling the binaries from source for AVX-512 cores Octopus no longer runs as normal, producing error:
'Phred: negative error
[2024-07-15 12:55:12] probability -…
-
Hi,
I'm trying to use Pisces to call a tumour-only sample. I'm using the following command:
```shell
$ dotnet Pisces.dll -bam tumour.bam \
-CallMNVs false -g hs37d5 -gVCF false \
-i h…
-
When the FILTER column in a VCF ".", is that a PASS variant or not or something else?
Motivation: I was using `pysam`'s `VariantRecord` and noticed that when the VCF has `"."` in the FILTER column,…
-
The Mutect2 WDL in the repo has a near copy of the funcotator WDL. In the interests of consolidation for easier testing and so on, Mutect2 should call Funcotator as an imported task or subworkflow. R…