modules/duphold

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.

sortdupholdstructural variationdepth information

https://github.com/nf-core/modules/[...]/modules/nf-core/duphold

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`alignment_file`
`:file`

file containing alignments

`alignment_index`
`:file`

index of alignment file

`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_index`
`:file`

index of snp variants file

`fasta`
`:file`

fasta file

*.{fa,fasta,fna}

`fasta_fai`
`:file`

Index of fasta file

*.fai

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

The output VCF

*.vcf.gz

`versions_duphold`

`${task.process}`
`:string`

The name of the process

`duphold`
`:string`

The name of the tool

`duphold -h | sed -e "s/^version: //;q"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`duphold`
`:string`

The name of the tool

`duphold -h | sed -e "s/^version: //;q"`
`:eval`

The expression to obtain the version of the tool

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

modules/duphold

Description

Input

`meta`
`:map`

`alignment_file`
`:file`

`alignment_index`
`:file`

`sv_variants`
`:file`

`snp_variants`
`:file`

`snp_variants_index`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`versions_duphold`

`${task.process}`
`:string`

`duphold`
`:string`

`duphold -h | sed -e "s/^version: //;q"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`duphold`
`:string`

`duphold -h | sed -e "s/^version: //;q"`
`:eval`

Tools

duphold
MIT

maintainer

get in touch

modules/duphold

Description

Input

meta:map

alignment_file:file

alignment_index:file

sv_variants:file

snp_variants:file

snp_variants_index:file

fasta:file

fasta_fai:file

Output

vcf

meta:map

*.vcf.gz:file

versions_duphold

${task.process}:string

duphold:string

duphold -h | sed -e "s/^version: //;q":eval

Topics

versions

${task.process}:string

duphold:string

duphold -h | sed -e "s/^version: //;q":eval

Tools

duphold MIT

maintainer

get in touch

`meta`
`:map`

`alignment_file`
`:file`

`alignment_index`
`:file`

`sv_variants`
`:file`

`snp_variants`
`:file`

`snp_variants_index`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`versions_duphold`

`${task.process}`
`:string`

`duphold`
`:string`

`duphold -h | sed -e "s/^version: //;q"`
`:eval`

`versions`

`${task.process}`
`:string`

`duphold`
`:string`

`duphold -h | sed -e "s/^version: //;q"`
`:eval`

duphold
MIT