Clara Parabricks v3.0
3.0

JOINT CALLING OVERVIEW

NVIDIA Clara Parabricks Pipelines accelerated tools for joint calling

Combing 2 or 3 GVCF samples in a fast way

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$ pbrun triocombinegvcf --ref Ref.fa --in-gvcf father.g.vcf \ --in-gvcf mother.g.vcf --in-gvcf child.g.vcf \ --out-variants combined.g.vcf


COMPATIBLE CPU GATK4 COMMAND

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$ gatk CombineGVCFs -R Ref.fa -V father.g.vcf -V mother.g.vcf \ -V child.g.vcf -O combined.g.vcf


OPTIONS

--ref

(required) The reference file in fasta format.

--in-gvcf

(required) Path to g.vcf or g.vcf.gz file. Option can be used 2 or 3 times.

--out-variants

(required) Path to output merged g.vcf file.

Start a genomic database for multiple samples.

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$ pbrun creategenomicsdb --dir database_dir


OPTIONS

--dir

(required) Path to the directory which will serve as the genomic database.

Add samples to a genomic database.

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$ pbrun importgvcftodb --db-dir database_dir --in-gvcf input.g.vcf


OPTIONS

--db-dir

(required) Path to the directory which has the genomic database already initialized.

--in-gvcf

(required) Path to input g.vcf.gz file to be added to the database. This option can be repeated multiple times.

--num-threads

Defaults to 4.

Number of threads for worker.

Select variants from a database and create a gvcf.

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$ pbrun selectvariants --ref Ref.fa \ --db-dir database_dir \ --out-gvcf-dir gvcf_dir


OPTIONS

--ref

(required) Path to the reference file.

--db-dir

(required) Path to the directory which is the genomic database.

--out-gvcf-dir

(required) Path to output directory which will have all the gvcf with selected variants.

--num-threads

Defaults to 4.

Number of threads for worker.

© Copyright 2020, NVIDIA. Last updated on Sep 14, 2020.