modules/manta_somatic

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.

somaticwgswxspanelvcfstructural variantssmall indels

https://github.com/nf-core/modules/[...]/modules/nf-core/manta/somatic

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`input_normal`
`:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`input_index_normal`
`:file`

BAM/CRAM/SAM index file

*.{bai,crai,sai}

`input_tumor`
`:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`input_index_tumor`
`:file`

BAM/CRAM/SAM index file

*.{bai,crai,sai}

`target_bed`
`:file`

BED file containing target regions for variant calling

*.{bed}

`target_bed_tbi`
`:file`

Index for BED file containing target regions for variant calling

*.{bed.tbi}

`meta2`
`:map`

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

`fasta`
`:file`

Genome reference FASTA file

*.{fa,fasta}

`meta3`
`:map`

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

`fai`
`:file`

Genome reference FASTA index file

*.{fa.fai,fasta.fai}

`config`
`:file`

Manta configuration file

*.{ini,conf,config}

Output

name:type

description

pattern

`candidate_small_indels_vcf`

`meta`
`:map`

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

`*.candidate_small_indels.vcf.gz`
`:file`

Gzipped VCF file containing variants

*.{vcf.gz}

`candidate_small_indels_vcf_tbi`

`meta`
`:map`

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

`*.candidate_small_indels.vcf.gz.tbi`
`:file`

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

`candidate_sv_vcf`

`meta`
`:map`

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

`*.candidate_sv.vcf.gz`
`:file`

Gzipped VCF file containing variants

*.{vcf.gz}

`candidate_sv_vcf_tbi`

`meta`
`:map`

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

`*.candidate_sv.vcf.gz.tbi`
`:file`

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

`diploid_sv_vcf`

`meta`
`:map`

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

`*.diploid_sv.vcf.gz`
`:file`

Gzipped VCF file containing variants

*.{vcf.gz}

`diploid_sv_vcf_tbi`

`meta`
`:map`

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

`*.diploid_sv.vcf.gz.tbi`
`:file`

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

`somatic_sv_vcf`

`meta`
`:map`

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

`*.somatic_sv.vcf.gz`
`:file`

Gzipped VCF file containing variants

*.{vcf.gz}

`somatic_sv_vcf_tbi`

`meta`
`:map`

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

`*.somatic_sv.vcf.gz.tbi`
`:file`

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

`versions_manta`

`${task.process}`
`:string`

The name of the process

`manta`
`:string`

The name of the tool

`configManta.py --version`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`manta`
`:string`

The name of the tool

`configManta.py --version`
`:eval`

The expression to obtain the version of the tool

Tools

manta
GPL v3

Structural variant and indel caller for mapped sequencing data

github.com/Illumina/manta github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md https://github.com/Illumina/manta 10.1093/bioinformatics/btv710

modules/manta_somatic

Description

Input

meta:map

input_normal:file

input_index_normal:file

input_tumor:file

input_index_tumor:file

target_bed:file

target_bed_tbi:file

meta2:map

fasta:file

meta3:map

fai:file

config:file

Output

candidate_small_indels_vcf

meta:map

*.candidate_small_indels.vcf.gz:file

candidate_small_indels_vcf_tbi

meta:map

*.candidate_small_indels.vcf.gz.tbi:file

candidate_sv_vcf

meta:map

*.candidate_sv.vcf.gz:file

candidate_sv_vcf_tbi

meta:map

*.candidate_sv.vcf.gz.tbi:file

diploid_sv_vcf

meta:map

*.diploid_sv.vcf.gz:file

diploid_sv_vcf_tbi

meta:map

*.diploid_sv.vcf.gz.tbi:file

somatic_sv_vcf

meta:map

*.somatic_sv.vcf.gz:file

somatic_sv_vcf_tbi

meta:map

*.somatic_sv.vcf.gz.tbi:file

versions_manta

${task.process}:string

manta:string

configManta.py --version:eval

Topics

versions

${task.process}:string

manta:string

configManta.py --version:eval

Tools

manta GPL v3

included in

maintainers

get in touch

`meta`
`:map`

`input_normal`
`:file`

`input_index_normal`
`:file`

`input_tumor`
`:file`

`input_index_tumor`
`:file`

`target_bed`
`:file`

`target_bed_tbi`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`config`
`:file`

`candidate_small_indels_vcf`

`meta`
`:map`

`*.candidate_small_indels.vcf.gz`
`:file`

`candidate_small_indels_vcf_tbi`

`meta`
`:map`

`*.candidate_small_indels.vcf.gz.tbi`
`:file`

`candidate_sv_vcf`

`meta`
`:map`

`*.candidate_sv.vcf.gz`
`:file`

`candidate_sv_vcf_tbi`

`meta`
`:map`

`*.candidate_sv.vcf.gz.tbi`
`:file`

`diploid_sv_vcf`

`meta`
`:map`

`*.diploid_sv.vcf.gz`
`:file`

`diploid_sv_vcf_tbi`

`meta`
`:map`

`*.diploid_sv.vcf.gz.tbi`
`:file`

`somatic_sv_vcf`

`meta`
`:map`

`*.somatic_sv.vcf.gz`
`:file`

`somatic_sv_vcf_tbi`

`meta`
`:map`

`*.somatic_sv.vcf.gz.tbi`
`:file`

`versions_manta`

`${task.process}`
`:string`

`manta`
`:string`

`configManta.py --version`
`:eval`

`versions`

`${task.process}`
`:string`

`manta`
`:string`

`configManta.py --version`
`:eval`

manta
GPL v3