https://github.com/dohlee/snakemake-gatk
:snake::wrench: Snakemake wrappers for GATK.
https://github.com/dohlee/snakemake-gatk
bioinformatics-analysis bioinformatics-pipeline gatk reproducible-research snakemake snakemake-workflows
Last synced: 3 months ago
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:snake::wrench: Snakemake wrappers for GATK.
- Host: GitHub
- URL: https://github.com/dohlee/snakemake-gatk
- Owner: dohlee
- Created: 2018-06-12T04:52:23.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2021-05-27T06:53:21.000Z (about 5 years ago)
- Last Synced: 2025-08-22T08:49:52.874Z (10 months ago)
- Topics: bioinformatics-analysis, bioinformatics-pipeline, gatk, reproducible-research, snakemake, snakemake-workflows
- Language: Python
- Homepage:
- Size: 49.8 KB
- Stars: 4
- Watchers: 1
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# snakemake-gatk
Snakemake wrappers for GATK.
## Requirements
- [GATK 4.0.8.1](https://software.broadinstitute.org/gatk/download/)
- Executable `gatk` in `$PATH`
## Recommended
To utilize [public resources](https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0) of Broad Institute, using **hg38 reference genome** (which can also be downloaded at [public resources](https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0)) is higly recommended. The link may get outdated by any time, so please refer to the official website of GATK to get the latest version of the resources. (Last updated: 2018.08.23)
## Available wrappers
- **cnv**: copy number variant discovery
- [create-read-count-panel-of-normals](gatk/cnv/create-read-count-panel-of-normals): wrapper for [CreateReadCountPanelOfNormals](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_copynumber_CreateReadCountPanelOfNormals.php)
- [denoise-read-counts](gatk/cnv/denoise-read-counts): wrapper for [DenoiseReadCounts](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_copynumber_DenoiseReadCounts.php)
- **coverage**: count reads
- [collect-read-counts](gatk/coverage/collect-read-counts): wrapper for [CollectReadCounts](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_copynumber_CollectReadCounts.php)
- [get-pileup-summaries](gatk/coverage/get-pileup-summaries): wrapper for [GetPileupSummaries](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_contamination_GetPileupSummaries.php)
- **intervals**: manipulate list of genomic intervals
- [preprocess-intervals](gatk/intervals/preprocess-intervals): wrapper for [PreprocessIntervals](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_copynumber_PreprocessIntervals.php)
- **misc**: miscellaneous
- [index-feature-file](gatk/misc/index-feature-file): wrapper for [IndexFeatureFile](https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.3.0/org_broadinstitute_hellbender_tools_IndexFeatureFile.php)
- [**mutect2**](gatk/mutect2): call somatic SNPs and indels
- [tumor-normal](gatk/mutect2/tumor-normal): wrapper for [Mutect2 with tumor & normal sample](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php)
- [tumor-only](gatk/mutect2/tumor-only): wrapper for [Mutect2 with single sample](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php)
- **preprocessing**: preprocess aligned read files
- [mark-duplicates](gatk/preprocessing/mark-duplicates): wrapper for [MarkDuplicates](https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.4.0/picard_sam_markduplicates_MarkDuplicates.php)
- [base-recalibrator](gatk/preprocessing/base-recalibrator): wrapper for [BaseRecalibrator](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_bqsr_BaseRecalibrator.php)
- [apply-bqsr](gatk/preprocessing/apply-bqsr): wrapper for [ApplyBQSR](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_bqsr_ApplyBQSR.php)
- **qc**: quality control
- [calculate-contamination](gatk/qc/calculate-contamination): wrapper for [CalculateContamination](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_contamination_CalculateContamination.php)
- **reference**: manipulate FASTA references
- [create-sequence-dictionary](gatk/reference/create-sequence-dictionary): wrapper for [CreateSequenceDictionary (Picard)](https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.3.0/picard_sam_CreateSequenceDictionary.php)
- **variant-filtering**: reduce the number of false-positive variant calls
- [create-somatic-panel-of-normals](gatk/variant-filtering/create-somatic-panel-of-normals): wrapper for [CreateSomaticPanelOfNormals](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_CreateSomaticPanelOfNormals.php)
- **variant-manipulation**: deal with VCF files.
- [select-variants](gatk/variant-manipulation/select-variants): wrapper for [SelectVariants](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_variantutils_SelectVariants.php)