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

interval_file: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:file

Variant file.

*.vcf

versions

versions.yml: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/4.0.1/documentation
maintainer
Github user bsiranosian
get in touch
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