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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 ]
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- input :
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type : file
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description : BAM/CRAM/SAM file. For joint calling use a list of files.
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pattern : "*.{bam,cram,sam}"
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- index :
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type : file
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description : BAM/CRAM/SAM index file. For joint calling use a list of files.
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pattern : "*.{bai,crai,sai}"
- fasta :
type : file
description : Genome reference FASTA file
pattern : "*.{fa,fasta}"
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- fasta_fai :
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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"
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- "@ramprasadn"