name: deepvariant description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data keywords: - variant calling - machine learning tools: - deepvariant: description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "https://doi.org/10.1038/nbt.4235" licence: ['BSD-3-clause'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM file pattern: "*.bam" - bai: type: file description: Index of BAM file pattern: "*.bai" - fasta: type: file description: The reference fasta file pattern: "*.fasta" - fai: type: file description: Index of reference fasta file pattern: "*.fai" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: type: file description: Compressed VCF file pattern: "*.vcf.gz" - gvcf: type: file description: Compressed GVCF file pattern: "*.g.vcf.gz" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@abhi18av"