name: sentieon_applyvarcal
description: |
  Apply a score cutoff to filter variants based on a recalibration table.
  Sentieon's Aplyvarcal 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 previous step VarCal and a target sensitivity value.
  https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm
keywords:
  - sentieon
  - applyvarcal
  - varcal
  - VQSR
tools:
  - sentieon:
      description: |
        Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.
        Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
      homepage: https://www.sentieon.com/
      documentation: https://www.sentieon.com/

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"
  - vcf_tbi:
      type: file
      description: tabix 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"
  - recal_index:
      type: file
      description: Index file for the recalibration file.
      pattern: ".recal.idx"
  - tranches:
      type: file
      description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.
      pattern: ".tranches"
  - meta2:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.fasta"
  - meta3:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - fai:
      type: file
      description: Index of reference fasta file
      pattern: "*.fasta.fai"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - 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:
  - "@assp8200"
