Description

NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples. [ id:‘test’, tumor_id:‘tumor’, normal_id:‘normal’ ]

tumor_bam:file

bam file for tumor sample.

*.bam

tumor_bam_index:file

(Optional) bai index corresponding to tumor bam file. Only required if intervals are provided.

*.bam

normal_bam:file

(Optional) bam file for normal sample in tumor-vs-normal calling.

*.bam

normal_bam_index:file

(Optional) bai index corresponding to normal bam file. Only required if intervals are provided.

*.bam

interval_file:file

(Optional) 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:‘homo_sapiens’ ]

fasta:file

reference fasta - must be unzipped.

*.fasta

panel_of_normals:file

(Optional) pannel of normals file.

*.vcf.gz

panel_of_normals_index:file

(Optional) tbi index corresponding to pannel of normals file.

*.tbi

Output

name:type
description
pattern

vcf

meta:map

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

*.vcf.gz:file

Compressed variants file. Will include an annoted vcf file if pannel of normals is used.

*.vcf.gz

stats

meta:map

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

*.vcf.gz.stats:file

Variant statistics.

*.vcf.gz.stats

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