modules/deepvariant_rundeepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

variant callingmachine learningneural network

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

Description

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM file

*.bam/cram

`index`
`:file`

Index of BAM/CRAM file

*.bai/crai

`intervals`
`:file`

file containing intervals

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fasta`
`:file`

The reference fasta file

*.fasta

`meta3`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fai`
`:file`

Index of reference fasta file

*.fai

`meta4`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`gzi`
`:file`

GZI index of reference fasta file

*.gzi

`meta5`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`par_bed`
`:file`

BED file containing PAR regions

*.bed

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`${prefix}.vcf.gz`
`:file`

Compressed VCF file

*.vcf.gz

`vcf_index`

`meta`
`:map`

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

`${prefix}.vcf.gz.{tbi,csi}`
`:file`

Tabix index file of compressed VCF

*.vcf.gz.{tbi,csi}

`gvcf`

`meta`
`:map`

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

`${prefix}.g.vcf.gz`
`:file`

Compressed GVCF file

*.g.vcf.gz

`gvcf_index`

`meta`
`:map`

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

`${prefix}.g.vcf.gz.{tbi,csi}`
`:file`

Tabix index file of compressed GVCF

*.g.vcf.gz.{tbi,csi}

`report`

`meta`
`:map`

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

`${prefix}.visual_report.html`
`:file`

Visual report in HTML format

*.html

`versions_deepvariant`

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

The process the versions were collected from

`deepvariant`
`:string`

The tool name

`/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`deepvariant`
`:string`

The tool name

`/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'`
`:eval`

The expression to obtain the version of the tool

Tools

deepvariant
BSD-3-clause

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

github.com/google/deepvariant 10.1038/nbt.4235

modules/deepvariant_rundeepvariant

Description

Input

meta:map

input:file

index:file

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

gzi:file

meta5:map

par_bed:file

Output

vcf

meta:map

${prefix}.vcf.gz:file

vcf_index

meta:map

${prefix}.vcf.gz.{tbi,csi}:file

gvcf

meta:map

${prefix}.g.vcf.gz:file

gvcf_index

meta:map

${prefix}.g.vcf.gz.{tbi,csi}:file

report

meta:map

${prefix}.visual_report.html:file

versions_deepvariant

${task.process}:string

deepvariant:string

/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //':eval

Topics

versions

${task.process}:string

deepvariant:string

/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //':eval

Tools

deepvariant BSD-3-clause

included in

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`gzi`
`:file`

`meta5`
`:map`

`par_bed`
`:file`

`vcf`

`meta`
`:map`

`${prefix}.vcf.gz`
`:file`

`vcf_index`

`meta`
`:map`

`${prefix}.vcf.gz.{tbi,csi}`
`:file`

`gvcf`

`meta`
`:map`

`${prefix}.g.vcf.gz`
`:file`

`gvcf_index`

`meta`
`:map`

`${prefix}.g.vcf.gz.{tbi,csi}`
`:file`

`report`

`meta`
`:map`

`${prefix}.visual_report.html`
`:file`

`versions_deepvariant`

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

`deepvariant`
`:string`

`/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'`
`:eval`

`versions`

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

`deepvariant`
`:string`

`/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'`
`:eval`

deepvariant
BSD-3-clause