diff --git a/CHANGELOG.md b/CHANGELOG.md index c9714a251..60064c112 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/docs/usage.md b/docs/usage.md index 6a9183049..255856d86 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -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 | ## How to run ASCAT with whole-exome sequencing data?