Description

NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant.

Input

name:type
description
pattern

meta

:map

Groovy Map containing tumor sample information - id must match read groups for this sample. [ id:‘test’]

input

:file

bam file for sample to be variant called.

*.bam

input_index

:file

bai index corresponding to input bam file. Only necessary if intervals are provided.

*.bai

intervals

:file

file or files containing genomic intervals for use in base quality score recalibration.

*.{bed,interval_list,picard,list,intervals}

ref_meta

:map

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

fasta

:file

reference fasta - must be unzipped.

*.fasta

Output

name:type
description
pattern

vcf

meta

:map

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

*.vcf.gz

:file

vcf file created with deepvariant (does not support .gz for normal vcf), optional

*.vcf

gvcf

meta

:map

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

*.g.vcf.gz

:file

bgzipped gvcf created with deepvariant, optional

*.g.vcf.gz

compatible_versions

compatible_versions.yml

:file

File containing info on compatible CPU-based software versions.

compatible_versions.yml

versions_parabricks

${task.process}

:string

The process the versions were collected from

parabricks

:string

The tool name

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

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

parabricks

:string

The tool name

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

: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