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Fix: Update variant calling tool - data type table in docs #1635

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Fix: Update variant calling tool - data type table in docs #1635

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c7bb43b
update table for implemented modes
famosab Aug 28, 2024
41bd3ca
format table
famosab Aug 28, 2024
1a9aa6e
format table
famosab Aug 28, 2024
c56ba54
update changelog
famosab Aug 28, 2024
fe06ed9
prettier
famosab Aug 28, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation
- [1628](https://github.com/nf-core/sarek/pull/1628) - Fix dbsnp channel mapping in germline variant calling subworkflow
- [1635](https://github.com/nf-core/sarek/pull/1635) - Fix docs to reflect variant calling tool - data type correctly

### Removed

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28 changes: 14 additions & 14 deletions docs/usage.md
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Expand Up @@ -575,20 +575,20 @@ Sarek can be started at different points in the analysis by setting the paramete

This list is by no means exhaustive and it will depend on the specific analysis you would like to run. This is a suggestion based on the individual docs of the tools specifically for human genomes and a garden-variety sequencing run as well as what has been added to the pipeline.

| Tool | WGS | WES |  Panel |  Normal | Tumor | Somatic |
| :------------------------------------------------------------------------------------------------------ | :-: | :-: | :----: | :-----: | :---: | :-----: |
| [DeepVariant](https://github.com/google/deepvariant) | x | x | x | x | - | - |
| [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x |
| [GATK HaplotypeCaller](https://gatk.broadinstitute.org/hc/en-us/articles/5358864757787-HaplotypeCaller) | x | x | x | x | - | - |
| [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2) | x | x | x | - | x | x |
| [mpileup](https://www.htslib.org/doc/samtools-mpileup.html) | x | x | x | x | x | - |
| [Strelka](https://github.com/Illumina/strelka) | x | x | x | x | x | x |
| [Manta](https://github.com/Illumina/manta) | x | x | x | x | x | x |
| [TIDDIT](https://github.com/SciLifeLab/TIDDIT) | x | x | x | x | x | x |
| [ASCAT](https://github.com/VanLoo-lab/ascat) | x | x | - | - | - | x |
| [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x |
| [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x |
| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | - | x |
| Tool | WGS | WES |  Panel |  Germline | Tumor-Only | Somatic (Tumor-Normal) |
| :------------------------------------------------------------------------------------------------------ | :-: | :-: | :----: | :-------: | :--------: | :--------------------: |
| [DeepVariant](https://github.com/google/deepvariant) | x | x | x | x | - | - |
| [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x |
| [GATK HaplotypeCaller](https://gatk.broadinstitute.org/hc/en-us/articles/5358864757787-HaplotypeCaller) | x | x | x | x | - | - |
| [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2) | x | x | x | - | x | x |
| [mpileup](https://www.htslib.org/doc/samtools-mpileup.html) | x | x | x | x | x | - |
| [Strelka](https://github.com/Illumina/strelka) | x | x | x | x | - | x |
| [Manta](https://github.com/Illumina/manta) | x | x | x | x | x | x |
| [TIDDIT](https://github.com/SciLifeLab/TIDDIT) | x | x | x | x | x | x |
| [ASCAT](https://github.com/VanLoo-lab/ascat) | x | x | - | - | - | x |
| [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x |
| [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x |
| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x |
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Suggested change
| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x |
| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | - | x |

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Not until we merged the PR from @bounlu

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Should we wait for that then?


## How to run ASCAT with whole-exome sequencing data?

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