Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

ref_meta (map)

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

input (file)

bam file for sample to be variant called.

*.bam

input_index (file)

(Optional) bai index corresponding to input bam file. Only necessary when using intervals.

*.bai

interval_file (file)

file or files containing genomic intervals.

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

fasta (file)

reference fasta - must be unzipped.

*.fasta

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions.

versions.yml

vcf (file)

variant file.

*.vcf
maintainer
Github user bsiranosian
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

parabricks
custom

NVIDIA Clara Parabricks GPU-accelerated genomics tools

nvidia.com/en-us/clara/genomics docs.nvidia.com/clara/parabricks/4.2.0