name: gatk4_getpileupsummaries description: | Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD. keywords: - gatk4 - getpileupsumaries - readcountssummary - germlinevariantsites 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' ] - bam: type: file description: BAM file to be summarised. pattern: "*.bam" - bai: type: file description: BAM file index. pattern: "*.bam.bai" - variants: type: file description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified. pattern: "*.vcf.gz" - variants_idx: type: file description: Index file for the germline resource. pattern: "*.vcf.gz.tbi" - sites: type: file description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically. pattern: "*.interval_list" output: - pileup: type: file description: File containing the pileup summary table. pattern: "*.pileups.table" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@GCJMackenzie"