Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

bam file for sample to be variant called.

*.bam

input_index{:bash}

:file

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

*.bai

interval_file{:bash}

:file

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

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

ref_meta{: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.gz{:bash}

:file

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

*.vcf

gvcf{:bash}

meta{:bash}

:map

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

*.g.vcf.gz{:bash}

:file

bgzipped gvcf created with deepvariant, optional

*.g.vcf.gz

compatible_versions{:bash}

compatible_versions.yml{:bash}

:file

File containing info on compatible CPU-based software versions.

compatible_versions.yml

versions{:bash}

versions.yml{:bash}

:file

File containing software versions.

versions.yml

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
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