Description

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

Input

name:type
description
pattern

meta

:map

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

tumor_bam

:file

bam file for tumor sample.

*.bam

tumor_bam_index

:file

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

*.{bai,csi}

normal_bam

:file

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

*.bam

normal_bam_index

:file

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

*.{bai,csi}

intervals

:file

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

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

meta2

:map

Groovy Map containing reference and index information [ id:‘homo_sapiens’ ]

fasta

:file

reference fasta - must be unzipped.

*.fasta

fasta_fai

:file

(Optional) reference fasta index.

*.fai

panel_of_normals

:file

(Optional) bgzipped panel of normals file. When provided, the module runs prepon, passes it to mutectcaller via –pon and annotates the output with postpon. Its header must contain only contigs present in the reference, otherwise prepon fails with “Chromosome number of pon file doesn’t match reference” (see bcftools reheader --fai). Do not add –pon via ext.args.

*.vcf.gz

panel_of_normals_index

:file

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

*.tbi

germline_resource

:file

(Optional) bgzipped population VCF of germline sequencing containing allele fractions, passed to mutectcaller via –mutect-germline-resource.

*.vcf.gz

germline_resource_index

:file

(Optional) tbi index corresponding to the germline resource file. Copied to <germline_resource>.tbi if named differently.

*.tbi

alleles

:file

(Optional) bgzipped VCF of alleles to force-call regardless of evidence, passed to mutectcaller via –mutect-alleles.

*.vcf.gz

alleles_index

:file

(Optional) tbi index corresponding to the alleles file. Copied to .tbi if named differently.

*.tbi

Output

name:type
description
pattern

vcf

meta

:map

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

${prefix}.vcf.gz

:file

Compressed variants file. Will include an annotated vcf file if panel of normals is used.

*.vcf.gz

tbi

meta

:map

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

${prefix}.vcf.gz.tbi

:file

Tabix index of the compressed variants file.

*.vcf.gz.tbi

stats

meta

:map

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

${prefix}.vcf.gz.stats

:file

Variant statistics.

*.vcf.gz.stats

f1r2

meta

:map

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

${prefix}.f1r2.tar.gz

:file

(Optional) F1R2 counts for learnreadorientationmodel, written when –mutect-f1r2-tar-gz ${prefix}.f1r2.tar.gz is set via ext.args.

*.f1r2.tar.gz

compatible_versions

compatible_versions.yml

:file

File containing info on compatible CPU-based software versions.

compatible_versions.yml

versions_parabricks

${task.process}

:string

The process the versions were collected from

parabricks

:string

The tool name

pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

parabricks

:string

The tool name

pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'

:string

The command used to generate the version of the tool

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
Ask a question on Slack Open an issue on GitHub