modules/svtyper_svtyper

SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data

svstructural variantsgenotyping

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

Description

SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`bam_index`
`:file`

Index of the BAM/CRAM/SAM file

*.{bai,crai,sai}

`vcf`
`:file`

Matching VCF of alignments

*.vcf

`meta2`
`:map`

Groovy Map containing sample information for FASTA file e.g. [ id:‘fasta’]

`fasta`
`:file`

FASTA file used to generate alignments

*.{fa,fasta}

`meta3`
`:map`

Groovy Map containing sample information for FASTA file e.g. [ id:‘fasta’]

`fai`
`:file`

FAI file used to generate alignments

*.{fai}

Output

name:type

description

pattern

`json`

`meta`
`:map`

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

`*.json`
`:file`

JSON file including Library information

*.json

`gt_vcf`

`meta`
`:map`

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

`*.vcf`
`:file`

Genotyped SVs

*.vcf

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

BAM file with

*.bam

`versions_svtyper`

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

The name of the process

`svtyper`
`:string`

The name of the tool

`svtyper -h 2>&1 | grep 'version:' | sed 's/^version: v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`svtyper`
`:string`

The name of the tool

`svtyper -h 2>&1 | grep 'version:' | sed 's/^version: v//'`
`:eval`

The expression to obtain the version of the tool

Tools

svtyper
MIT

Compute genotype of structural variants based on breakpoint depth

github.com/hall-lab/svtyper 10.1038/nmeth.3505

modules/svtyper_svtyper

Description

Input

`meta`
`:map`

`bam`
`:file`

`bam_index`
`:file`

`vcf`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

Output

`json`

`meta`
`:map`

`*.json`
`:file`

`gt_vcf`

`meta`
`:map`

`*.vcf`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_svtyper`

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

`svtyper`
`:string`

`svtyper -h 2>&1 | grep 'version:' | sed 's/^version: v//'`
`:eval`

Topics

`versions`

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

`svtyper`
`:string`

`svtyper -h 2>&1 | grep 'version:' | sed 's/^version: v//'`
`:eval`

Tools

svtyper
MIT

maintainer

get in touch

modules/svtyper_svtyper

Description

Input

meta :map

bam :file

bam_index :file

vcf :file

meta2 :map

fasta :file

meta3 :map

fai :file

Output

json

meta :map

*.json :file

gt_vcf

meta :map

*.vcf :file

bam

meta :map

*.bam :file

versions_svtyper

${task.process} :string

svtyper :string

svtyper -h 2>&1 | grep 'version:' | sed 's/^version: v//' :eval

Topics

versions

${task.process} :string

svtyper :string

svtyper -h 2>&1 | grep 'version:' | sed 's/^version: v//' :eval

Tools

svtyperMIT

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bam_index`
`:file`

`vcf`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`json`

`meta`
`:map`

`*.json`
`:file`

`gt_vcf`

`meta`
`:map`

`*.vcf`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_svtyper`

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

`svtyper`
`:string`

`svtyper -h 2>&1 | grep 'version:' | sed 's/^version: v//'`
`:eval`

`versions`

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

`svtyper`
`:string`

`svtyper -h 2>&1 | grep 'version:' | sed 's/^version: v//'`
`:eval`

svtyper
MIT