name: gatk4_combinegvcfs description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file keywords: - gvcf - gatk4 - vcf - combinegvcfs - Short_Variant_Discovery tools: - gatk4: description: Genome Analysis Toolkit (GATK4). 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/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] input: - fasta: type: file description: The reference fasta file pattern: "*.fasta" - fai: type: file description: FASTA index file pattern: "*.{fai}" - dict: type: file description: FASTA dictionary file pattern: "*.{dict}" - vcf: type: file description: Compressed VCF files pattern: "*.vcf.gz" - vcf_idx: type: file description: VCF Index file pattern: "*.{fai}" output: - gvcf: type: file description: Compressed Combined GVCF file pattern: "*.combined.g.vcf.gz" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" - "@hseabolt"