Description

(DEPRECATED - see main.nf) 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{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file

*.bam/cram

index{:bash}

:file

Index of BAM/CRAM file

*.bai/crai

intervals{:bash}

:file

file containing intervals

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.fasta

meta3{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

*.fai

meta4{:bash}

:map

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

gzi{:bash}

:file

GZI index of reference fasta file

*.gzi

meta5{:bash}

:map

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

par_bed{:bash}

:file

BED file containing PAR regions

*.bed

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

${prefix}.vcf.gz{:bash}

:file

Compressed VCF file

*.vcf.gz

vcf_tbi{:bash}

meta{:bash}

:map

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

${prefix}.vcf.gz.tbi{:bash}

:file

Tabix index of compressed VCF file

*.vcf.gz.tbi

gvcf{:bash}

meta{:bash}

:map

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

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

:file

Compressed GVCF file

*.g.vcf.gz

gvcf_tbi{:bash}

meta{:bash}

:map

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

${prefix}.g.vcf.gz.tbi{:bash}

:file

Tabix index of compressed GVCF file

*.g.vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
included in
pacvarvariantcatalogue
maintainers
Github user abhi18av
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub