modules/gatk4_svannotate

Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF.

annotategatk4structural variantssvannotatevcf

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/svannotate

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

A VCF file created with a structural variant caller

*.vcf.gz

`tbi`
`:file`

The index file of the VCF

*.vcf.gz.tbi

`bed`
`:file`

Regions to limit the analysis to

*.bed

`non_coding_bed`
`:file`

File containing noncoding regions

*.bed

`meta2`
`:map`

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

`fasta`
`:file`

Optional - reference FASTA file needed when the input is a CRAM file

*.{fasta,fa}

`meta3`
`:map`

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

`fasta_fai`
`:file`

Optional - index of the reference FASTA file needed when the input is a CRAM file

*.fai

`meta4`
`:map`

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

`dict`
`:file`

Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file

*.dict

`meta5`
`:map`

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

`gtf`
`:file`

Optional - GTF file containing transcript information

*.gtf

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

The annotated structural variant VCF

*.vcf.gz

`tbi`

`meta`
`:map`

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

`*.vcf.gz.tbi`
`:file`

The index of the VCF

*.vcf.gz.tbi

`versions_gatk4`

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

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Tools

gatk4
BSD-3-clause

Genome Analysis Toolkit (GATK4)

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590

modules/gatk4_svannotate

Description

Input

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`bed`
`:file`

`non_coding_bed`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fasta_fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`gtf`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_gatk4`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Topics

`versions`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Tools

gatk4
BSD-3-clause

maintainer

get in touch

modules/gatk4_svannotate

Description

Input

meta:map

vcf:file

tbi:file

bed:file

non_coding_bed:file

meta2:map

fasta:file

meta3:map

fasta_fai:file

meta4:map

dict:file

meta5:map

gtf:file

Output

vcf

meta:map

*.vcf.gz:file

tbi

meta:map

*.vcf.gz.tbi:file

versions_gatk4

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Topics

versions

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Tools

gatk4 BSD-3-clause

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`bed`
`:file`

`non_coding_bed`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fasta_fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`gtf`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_gatk4`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

gatk4
BSD-3-clause