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:map

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

]

vcf:file

VCF file produces by Manta

*.vcf.gz

meta2:map

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

]

fasta:file

The reference fasta file

*.{fasta,fa,fna}

Output

name:type
description
pattern

vcf

meta:map

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

]

*.vcf.gz:file

VCF file with reformatted inversions

*.vcf.gz

tbi

meta:map

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

]

*.vcf.gz.tbi:file

TBI file produces by Manta

*.vcf.gz.tbi

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
variantbenchmarking
maintainer
Github user FriederikeHanssen
get in touch
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