Description

SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

aligment_file (file)

BAM/CRAM file

*.{bam,cram}

aligment_file_index (file)

Index of the BAM/CRAM file

*.{bai,crai}

sv_variants (file)

A variants file containing structural variants

*.{vcf,bcf}(.gz)?

snp_variants (file)

A variants file containing SNPs

*.{vcf,bcf}(.gz)?

snp_variants (file)

The index of the variants file containing SNPs

*.tbi

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 output VCF

*.vcf.gz
author
Github user nvnieuwk
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Tools

duphold
MIT

SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls.

github.com/brentp/duphold 10.1093/gigascience/giz040