name: gatk4_calculatecontamination description: | Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls. keywords: - gatk4 - calculatecontamination - cross-samplecontamination - getpileupsummaries - filtermutectcalls 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' ] - pileup: type: file description: File containing the pileups summary table of a tumor sample to be used to calculate contamination. pattern: "*.pileups.table" - matched: type: file description: File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input. pattern: "*.pileups.table" - segmentout: type: boolean description: specifies whether to output the segmentation table. output: - contamination: type: file description: File containing the contamination table. pattern: "*.contamination.table" - segmentation: type: file description: optional output table containing segmentation of tumor minor allele fractions. pattern: "*.segmentation.table" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@GCJMackenzie"