Description

NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test' ]

input{:bash}

:file

gvcf file for samples to be jointly genotyped.

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

meta2{:bash}

:map

Groovy Map containing reference information. [ id:‘test’]

fasta{:bash}

:file

reference fasta - must be unzipped.

*.fasta

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test' ]

*.vcf{:bash}

:file

vcf file after gvcf conversion.

*.vcf

versions_parabricks{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

parabricks{:bash}

:string

The tool name

pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

parabricks{:bash}

:string

The tool name

pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'{:bash}

:string

The command used to generate the version of the tool

Tools

parabricks
custom

NVIDIA Clara Parabricks GPU-accelerated genomics tools

nvidia.com/en-us/clara/genomics docs.nvidia.com/clara/parabricks/latest
maintainer
Github user famosab
get in touch
Ask a question on Slack Open an issue on GitHub