name: gatk4_variantrecalibrator description: | Build a recalibration model to score variant quality for filtering purposes. It is highly recommended to follow GATK best practices when using this module, the gaussian mixture model requires a large number of samples to be used for the tool to produce optimal results. For example, 30 samples for exome data. For more details see https://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR- keywords: - VariantRecalibrator - gatk4 - recalibration_model 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 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] - vcf: type: file description: input vcf file containing the variants to be recalibrated pattern: "*.vcf.gz" - tbi: type: file description: tbi file matching with -vcf pattern: "*.vcf.gz.tbi" - 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: specify whether to use allele specific annotations pattern: "{true,false}" - resvcfs: type: list description: resource files to be used as truth, training and known sites resources, this imports the files into the module, file names are specified again in the resource_labels to be called via the command. pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz' - restbis: type: list description: tbis for the corresponding vcfs files to be used as truth, training and known resources. pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz.tbi' - reslabels: type: list description: labels for the resource files to be used as truth, training and known sites resources, label should include an identifier,which kind of resource(s) it is, prior value and name of the file. pattern: "hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38_chr21.vcf.gz" - annotation: type: list description: specify which annotations should be used for calculations. pattern: "['QD', 'MQ', 'FS', 'SOR']" - mode: type: string description: specifies which recalibration mode to employ (SNP is default, BOTH is intended for testing only) pattern: "{SNP,INDEL,BOTH}" - rscript: type: boolean description: specify whether to generate rscript.plot output file pattern: "{true,false}" output: - recal: type: file description: Output recal file used by ApplyVQSR pattern: "*.recal" - idx: type: file description: Index file for the recal output file pattern: "*.idx" - tranches: type: file description: Output tranches file used by ApplyVQSR pattern: "*.tranches" - plots: type: file description: Optional output rscript file to aid in visualization of the input data and learned model. pattern: "*plots.R" - version: type: file description: File containing software versions pattern: "*.versions.yml" authors: - "@GCJMackenzie"