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

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Dec 10, 2024
Merged

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
1ccf16b
Update docs/usage.md
FriederikeHanssen Dec 10, 2024
2cc694b
Merge branch 'dev' into doc
FriederikeHanssen Dec 10, 2024
e40d91d
[automated] Fix code linting
nf-core-bot Dec 10, 2024
ed95c83
move entry to correct section
FriederikeHanssen Dec 10, 2024
ae24b7f
Update CHANGELOG.md
FriederikeHanssen Dec 10, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed

- [1579](https://github.com/nf-core/sarek/pull/1579) - Update Sentieon usage docs
- [1635](https://github.com/nf-core/sarek/pull/1635) - Fix docs to reflect variant calling tool - data type correctly
- [1668](https://github.com/nf-core/sarek/pull/1668) - Add nf-test sharding CI
- [1669](https://github.com/nf-core/sarek/pull/1669) - Better nf-test pipeline level tests
- [1677](https://github.com/nf-core/sarek/pull/1677) - Migrate pytest aligner and pipeline default tests to nf-test
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30 changes: 15 additions & 15 deletions docs/usage.md
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Expand Up @@ -575,21 +575,21 @@ 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 |
| [lofreq](https://github.com/CSB5/lofreq) | 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 |
| 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 |
| [lofreq](https://github.com/CSB5/lofreq) | 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 |

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

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