name: gatk4_variantfiltration description: Filter variants keywords: - vcf - filter 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'] - vcf: type: list description: List of VCF(.gz) files pattern: "*.{vcf,vcf.gz}" - vcf_tbi: type: list description: List of VCF file indexes pattern: "*.{idx,tbi}" - fasta: type: file description: Fasta file of reference genome pattern: "*.fasta" - fai: type: file description: Index of fasta file pattern: "*.fasta.fai" - dict: type: file description: Sequence dictionary of fastea file pattern: "*.dict" output: - vcf: type: file description: Compressed VCF file pattern: "*.vcf.gz" - tbi: type: file description: Index of VCF file pattern: "*.vcf.gz.tbi" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@kevinmenden"