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Dear Chris,
I am trying to run the copyCat in the paired mode as follows.
```
copyCat::runPairedSampleAnalysis(
annotationDirectory="./annotations/",
…
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### Description
There is currently no updated, self-maintained resource to list exhaustively existing remote modules. The ITK remote group in the Doxygen documentation:
https://itk.org/Doxygen/htm…
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Hi,
I'm currently evaluating VarDict on a synthetic tumour dataset similar to the ICGC DREAM set. I'm using VarDict version 1.5.2 with the following commands:
Call variants:
```shell
$ VarDi…
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### Need
As a geneticist I want to see true variants and not false positive calls. Currently we have databases for annotating variants that are commonly observed as somatic in highly filtered T+N c…
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**CODE:**
hap.py 40X_deepvariant_illumina_tumor_only.vcf 40X_PEPPER_MARGIN_tumor_only.vcf -r /public/groups/vg/xkang12/data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta -o hap_result/
**I…
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Installation:
```
conda install -c bioconda manta
```
Usage:
```
configManta.py \
--normalBam normal.cram \
--tumorBam tumor.cram \
--referenceFasta genome.fa \
--runDir ${MY_MANTA_WORKD…
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Hi,
(Is it better to post this here or in the google group? As I'm not sure this is an issue, rather an operator error)
We have a project in which we want to include both germline and tumor sample…
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This issue is meant to track the necessary steps required to integrate [`neuropoly/TotalSpineSeg`](https://github.com/neuropoly/totalspineseg) into SCT.
> Context: https://github.com/neuropoly/tot…
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### Description
It has been mentioned previously that our current methods for detecting CNVs are not working very well for low tumor purity samples: https://github.com/Clinical-Genomics/project…
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### Have you checked the docs?
- [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [X] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules)
### …