name: gatk4_mutect2 description: Call somatic SNVs and indels via local assembly of haplotypes. keywords: - gatk4 - mutect2 - haplotype - somatic 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'] - input: type: list description: list of BAM files, also able to take CRAM as an input pattern: "*.{bam/cram}" - input_index: type: list description: list of BAM file indexes, also able to take CRAM indexes as an input pattern: "*.{bam.bai/cram.crai}" - which_norm: type: list description: optional list of sample headers contained in the normal sample bam files (these are required for tumor_normal_pair mode) pattern: "testN" - run_single: type: boolean description: Specify whether or not to run in tumor_single mode instead of tumor_normal_pair mode (will be ignored if run_pon is also true) pattern: "true/false" - run_pon: type: boolean description: Specify whether or not to run in panel_of_normal mode instead of tumor_normal_pair mode pattern: "true/false" - run_mito: type: boolean description: Specify whether or not to run in mitochondria-mode instead of tumor_normal_pair mode pattern: "true/false" - interval_label: type: string description: Specify the label used for mitochondrial chromosome when mutect2 is run in mitochondria mode. pattern: "chrM" - fasta: type: file description: The reference fasta file pattern: "*.fasta" - fastaidx: type: file description: Index of reference fasta file pattern: "fasta.fai" - dict: type: file description: GATK sequence dictionary pattern: "*.dict" - germline_resource: type: file description: Population vcf of germline sequencing, containing allele fractions. pattern: "*.vcf.gz" - germline_resource_idx: type: file description: Index file for the germline resource. pattern: "*.vcf.gz_tbi" - panel_of_normals: type: file description: vcf file to be used as a panel of normals. pattern: "*.vcf.gz" - panel_of_normals_idx: type: file description: Index for the panel of normals. pattern: "*.vcf.gz_tbi" output: - vcf: type: file description: compressed vcf file pattern: "*.vcf.gz" - tbi: type: file description: Index of vcf file pattern: "*vcf.gz.tbi" - stats: type: file description: Stats file that pairs with output vcf file pattern: "*vcf.gz.stats" - f1r2: type: file description: file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run) pattern: "*.f1r2.tar.gz" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@GCJMackenzie"