name: manta_germline description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. keywords: - somatic - wgs - wxs - panel - vcf - structural variants - small indels tools: - manta: description: Structural variant and indel caller for mapped sequencing data homepage: https://github.com/Illumina/manta documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ['GPL v3'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - input: type: file description: BAM/CRAM/SAM file. For joint calling use a list of files. pattern: "*.{bam,cram,sam}" - index: type: file description: BAM/CRAM/SAM index file. For joint calling use a list of files. pattern: "*.{bai,crai,sai}" - fasta: type: file description: Genome reference FASTA file pattern: "*.{fa,fasta}" - fasta_fai: type: file description: Genome reference FASTA index file pattern: "*.{fa.fai,fasta.fai}" - target_bed: type: file description: BED file containing target regions for variant calling pattern: "*.{bed}" - target_bed_tbi: type: file description: Index for BED file containing target regions for variant calling pattern: "*.{bed.tbi}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - candidate_small_indels_vcf: type: file description: Gzipped VCF file containing variants pattern: "*.{vcf.gz}" - candidate_small_indels_vcf_tbi: type: file description: Index for gzipped VCF file containing variants pattern: "*.{vcf.gz.tbi}" - candidate_sv_vcf: type: file description: Gzipped VCF file containing variants pattern: "*.{vcf.gz}" - candidate_sv_vcf_tbi: type: file description: Index for gzipped VCF file containing variants pattern: "*.{vcf.gz.tbi}" - diploid_sv_vcf: type: file description: Gzipped VCF file containing variants pattern: "*.{vcf.gz}" - diploid_sv_vcf_tbi: type: file description: Index for gzipped VCF file containing variants pattern: "*.{vcf.gz.tbi}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@maxulysse" - "@ramprasadn"