Description

Convert SV calls to a standardized format.

Input

Name (Type)
Description
Pattern

args (map)

Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes.

{  
  [  
    "args": "",  
    "caller": "delly" // Should be either delly, lumpy, manta, wham or melt  
  ]  
}

meta (map)

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

]

vcf (file)

A gzipped VCF file to be standardized

*.vcf.gz

fasta_fai (file)

Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)

*.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

standardized_vcf (file)

A gzipped version of the standardized VCF file

*.std.vcf.gz
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