snakemake-gatk

Snakemake wrappers for GATK.

Requirements

• GATK 4.0.8.1
• Executable gatk in $PATH

Recommended

To utilize public resources of Broad Institute, using hg38 reference genome (which can also be downloaded at public resources) 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 The link may get outdated by any time, so please refer to the official website of GATK to get the latest version of the resources.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: wrapper for CreateReadCountPanelOfNormals
  • denoise-read-counts: wrapper for DenoiseReadCounts
• coverage: count reads
  • collect-read-counts: wrapper for CollectReadCounts
  • get-pileup-summaries: wrapper for GetPileupSummaries
• intervals: manipulate list of genomic intervals
  • preprocess-intervals: wrapper for PreprocessIntervals
• misc: miscellaneous
  • index-feature-file: wrapper for IndexFeatureFile
• mutect2: call somatic SNPs and indels
  • tumor-normal: wrapper for Mutect2 with tumor & normal sample
  • tumor-only: wrapper for Mutect2 with single sample
• preprocessing: preprocess aligned read files
  • mark-duplicates: wrapper for MarkDuplicates
  • base-recalibrator: wrapper for BaseRecalibrator
  • apply-bqsr: wrapper for ApplyBQSR
• qc: quality control
  • calculate-contamination: wrapper for CalculateContamination
• reference: manipulate FASTA references
  • create-sequence-dictionary: wrapper for CreateSequenceDictionary (Picard)
• variant-filtering: reduce the number of false-positive variant calls
  • create-somatic-panel-of-normals: wrapper for CreateSomaticPanelOfNormals
• variant-manipulation: deal with VCF files.
  • select-variants: wrapper for SelectVariants