name: gatk4_applyvqsr
description: |
  Apply a score cutoff to filter variants based on a recalibration table.
  AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).
  Specifically, it applies filtering to the input variants based on the recalibration table produced
  in the first step by VariantRecalibrator and a target sensitivity value.
keywords:
  - gatk4
  - applyvqsr
  - VQSR
tools:
  - gatk4:
      description: |
        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
        with a primary focus on variant discovery and genotyping. Its powerful processing engine
        and high-performance computing features make it capable of taking on projects of any size.
      homepage: https://gatk.broadinstitute.org/hc/en-us
      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
      doi: 10.1158/1538-7445.AM2017-3590
      licence: ['Apache-2.0']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - vcf:
      type: file
      description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.
      pattern: "*.vcf"
  - tbi:
      type: file
      description: Tbi index for the input vcf file.
      pattern: "*.vcf.tbi"
  - recal:
      type: file
      description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.
      pattern: "*.recal"
  - recalidx:
      type: file
      description: Index file for the recalibration file.
      pattern: ".recal.idx"
  - tranches:
      type: boolean
      description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.
      pattern: ".tranches"
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.fasta"
  - fai:
      type: file
      description: Index of reference fasta file
      pattern: "*.fasta.fai"
  - dict:
      type: file
      description: GATK sequence dictionary
      pattern: "*.dict"
  - allelespecific:
      type: boolean
      description: Whether or not to run ApplyVQSR in allele specific mode, this should be kept the same as the stage 1 VariantRecalibrator run.
      pattern: "{true,false}"
  - truthsensitivity:
      type: double
      description: Value to be used as the truth sensitivity cutoff score.
      pattern: "99.0"
  - mode:
      type: String
      description: Specifies which recalibration mode to employ, should be the same as the stage 1 VariantRecalibrator run. (SNP is default, BOTH is intended for testing only)
      pattern: "{SNP,INDEL,BOTH}"

output:
  - vcf:
      type: file
      description: compressed vcf file containing the recalibrated variants.
      pattern: "*.vcf.gz"
  - tbi:
      type: file
      description: Index of recalibrated vcf file.
      pattern: "*vcf.gz.tbi"
  - versions:
      type: file
      description: File containing software versions.
      pattern: "versions.yml"

authors:
  - "@GCJMackenzie"