Description

Convert an RdTest-formatted bed to the standard VCF format.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

An RdTest-formatted bed

*.bed

samples (file)

A text file containing the names of all samples that need to be added to the VCF

*.txt

fasta_fai (file)

The reference file of a FASTA file containing the contigs

*.fai

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)

The converted VCF

*.vcf.gz

tbi (file)

The index of the converted VCF

*.vcf.gz.tbi
author
Github user nvnieuwk
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Tools

svtk
MIT

Utilities for consolidating, filtering, resolving, and annotating structural variants.

github.com/broadinstitute/gatk-sv[...]src/svtk 10.1038/s41586-020-2287-8