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

]

input (file)

BAM/CRAM file

*.bam/cram

index (file)

Index of BAM/CRAM file

*.bai/crai

interval (file)

Interval file for targeted regions

*.bed

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

Output

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

Compressed VCF file

*.vcf.gz

gvcf (file)

Compressed GVCF file

*.g.vcf.gz

version (file)

File containing software version

*.{version.txt}
included in
raredisease sarek variantcatalogue
maintainers
Github user abhi18av
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub

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