NVIDIA Clara Parabricks Pipelines:Variant Processing: 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
Path to the reference file.
Path to the input bam file.
Path to the input vcf file.
Path to the output vcf file.
Path of a non-default parabricks model file for cnnscorevariants.
Defaults to number of GPUs in the system.
Number of GPUs to use for a run.
Which GPU devices to use for a run. By default, all GPU devices will be used. To set specific GPU devices, enter a comma-separated list of GPU device numbers.