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

meta (map)

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

vcf (file)

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

*.vcf.gz

stats (file)

Variant statistics.

*.vcf.gz.stats

versions (file)

File containing software versions.

versions.yml
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/4.0.1