cnnscorevariants

GPU accelerated CNNScorevariants

Generate variant scores using a Convolutional Neural Network.

Quick Start

CLI

$ pbrun cnnscorevariants --ref Ref.fa \
--in-bam sample.bam \
--in-vcf sample.vcf \
--out-vcf output.vcf

Compatible GATK4 Command

gatk CNNScoreVariants -R Ref.fa \
-I sample.bam \
-V sample.vcf \
-O output.vcf \
--tensor-type read_tensor

Post-Analysis Filtering

CNNScoreVariants generates an info field for each variant called CNN_2D. This field can be used to create filters for each variant by running the GATK4 tool FilterVariantTranches on the CNNScoreVariants output.

Options

Option

Description

--ref (required)

Path to the reference file.

--in-bam (required)

Path to the input bam file.

--in-vcf (required)

Path to the input vcf file.

--out-vcf (required)

Path to the output vcf file.

--pb-model-file

Path of a non-default parabricks model file for cnnscorevariants.

--num-gpus

Defaults to number of GPUs in the system.
Number of GPUs to use for a run.