Description

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

VCF file produces by Manta

*.vcf.gz

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.{fasta,fa,fna}

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

VCF file with reformatted inversions

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:file

TBI file produces by Manta

*.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

versions_samtools{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools --version | head -1 | sed -e s'/samtools //'{: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

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools --version | head -1 | sed -e s'/samtools //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
variantbenchmarking
maintainer
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub