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:map

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

]

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

]

*.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}

diploid_sv_vcf

meta:map

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

]

*.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

]

*.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

]

*.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

]

*.somatic_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

included in
rnadnavar sarek
maintainers
Github user FriederikeHanssen
Github user nvnieuwk
get in touch
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