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{:bash}

:map

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

alignment_file{:bash}

:file

file containing alignments

alignment_index{:bash}

:file

index of alignment file

sv_variants{:bash}

:file

A variants file containing structural variants

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

snp_variants{:bash}

:file

A variants file containing SNPs

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

snp_variants_index{:bash}

:file

index of snp variants file

fasta{:bash}

:file

fasta file

*.{fa,fasta,fna}

fasta_fai{:bash}

:file

Index of fasta file

*.fai

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

The output VCF

*.vcf.gz

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
maintainer
Github user nvnieuwk
get in touch
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