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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

vcf (file)

VCF file with reformatted inversions

*.vcf.gz

tbi (file)

TBI file produces by Manta

*.vcf.gz.tbi
included in
variantbenchmarking
maintainer
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub

Tools