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:map

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

]

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

]

${prefix}.vcf.gz:file

Compressed VCF file

*.vcf.gz

vcf_tbi

meta:map

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

]

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

Tabix index of compressed VCF file

*.vcf.gz.tbi

gvcf

meta:map

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

]

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

Compressed GVCF file

*.g.vcf.gz

gvcf_tbi

meta:map

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

]

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

Tabix index of compressed GVCF file

*.g.vcf.gz.tbi

versions

versions.yml: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
pacvar variantcatalogue
Github user abhi18av
Github user ramprasadn
Ask a question on Slack Open an issue on GitHub