modules/manta_tumoronly

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/tumoronly

Description

Input

name:type

description

pattern

`meta:map`

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

]

`input:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`input_index: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

]

`*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

]

`*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

]

`*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

]

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

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

`tumor_sv_vcf`

`meta:map`

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

]

`*tumor_sv.vcf.gz:file`

Gzipped VCF file containing variants

*.{vcf.gz}

`tumor_sv_vcf_tbi`

`meta:map`

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

]

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

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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_tumoronly

Description

Input

`meta:map`

`input:file`

`input_index: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`

`tumor_sv_vcf`

`meta:map`

`*tumor_sv.vcf.gz:file`

`tumor_sv_vcf_tbi`

`meta:map`

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

`versions`

`versions.yml:file`

Tools

manta
GPL v3

included in

maintainers

get in touch

modules/manta_tumoronly

Description

Input

meta:map

input:file

input_index: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

tumor_sv_vcf

meta:map

*tumor_sv.vcf.gz:file

tumor_sv_vcf_tbi

meta:map

*tumor_sv.vcf.gz.tbi:file

versions

versions.yml:file

Tools

manta GPL v3

included in

maintainers

get in touch

`meta:map`

`input:file`

`input_index: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`

`tumor_sv_vcf`

`meta:map`

`*tumor_sv.vcf.gz:file`

`tumor_sv_vcf_tbi`

`meta:map`

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

`versions`

`versions.yml:file`

manta
GPL v3