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

meta (map)

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

]

candidate_small_indels_vcf (file)

Gzipped VCF file containing variants

*.{vcf.gz}

candidate_small_indels_vcf_tbi (file)

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

candidate_sv_vcf (file)

Gzipped VCF file containing variants

*.{vcf.gz}

candidate_sv_vcf_tbi (file)

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

diploid_sv_vcf (file)

Gzipped VCF file containing variants

*.{vcf.gz}

diploid_sv_vcf_tbi (file)

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

somatic_sv_vcf (file)

Gzipped VCF file containing variants

*.{vcf.gz}

somatic_sv_vcf_tbi (file)

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

versions (file)

File containing software versions

versions.yml