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.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

input_normal{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index_normal{:bash}

:file

BAM/CRAM/SAM index file

*.{bai,crai,sai}

input_tumor{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index_tumor{:bash}

:file

BAM/CRAM/SAM index file

*.{bai,crai,sai}

target_bed{:bash}

:file

BED file containing target regions for variant calling

*.{bed}

target_bed_tbi{:bash}

:file

Index for BED file containing target regions for variant calling

*.{bed.tbi}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fasta{:bash}

:file

Genome reference FASTA file

*.{fa,fasta}

meta3{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fai{:bash}

:file

Genome reference FASTA index file

*.{fa.fai,fasta.fai}

config{:bash}

:file

Manta configuration file

*.{ini,conf,config}

Output

name:type
description
pattern

candidate_small_indels_vcf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.candidate_small_indels.vcf.gz{:bash}

:file

Gzipped VCF file containing variants

*.{vcf.gz}

candidate_small_indels_vcf_tbi{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.candidate_small_indels.vcf.gz.tbi{:bash}

:file

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

candidate_sv_vcf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.candidate_sv.vcf.gz{:bash}

:file

Gzipped VCF file containing variants

*.{vcf.gz}

candidate_sv_vcf_tbi{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.candidate_sv.vcf.gz.tbi{:bash}

:file

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

diploid_sv_vcf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.diploid_sv.vcf.gz{:bash}

:file

Gzipped VCF file containing variants

*.{vcf.gz}

diploid_sv_vcf_tbi{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.diploid_sv.vcf.gz.tbi{:bash}

:file

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

somatic_sv_vcf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.somatic_sv.vcf.gz{:bash}

:file

Gzipped VCF file containing variants

*.{vcf.gz}

somatic_sv_vcf_tbi{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.somatic_sv.vcf.gz.tbi{:bash}

:file

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

versions_manta{:bash}

${task.process}{:bash}

:string

The name of the process

manta{:bash}

:string

The name of the tool

configManta.py --version{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

manta{:bash}

:string

The name of the tool

configManta.py --version{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
rnadnavarsarek
maintainers
Github user FriederikeHanssen
Github user nvnieuwk
get in touch
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