GPU accelerated CNNScorevariants. Generate variant scores using a Convolutional Neural Network.
$ pbrun cnnscorevariants \
--ref Ref.fa \
--in-bam sample.bam \
--in-vcf sample.vcf \
--out-vcf output.vcf
gatk CNNScoreVariants -R Ref.fa \
-I sample.bam \
-V sample.vcf \
-O output.vcf \
--tensor-type read_tensor
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.
Run cnnscorevariants to generate variant scores using a Convolutional NeuralNetwork.
Input/Output file options
- --ref REF
-
Path to the reference file. (default: None)
Option is required.
- --in-bam IN_BAM
-
Path to the input BAM file. (default: None)
Option is required.
- --in-vcf IN_VCF
-
Path to the input VCF file. (default: None)
Option is required.
- --out-vcf OUT_VCF
-
Path to the output VCF file. (default: None)
Option is required.
- --pb-model-file PB_MODEL_FILE
-
Path of non-default parabricks model file for cnnscorevariants. (default: None)
Options specific to this tool
(none)
Common options:
- --logfile LOGFILE
-
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
- --tmp-dir TMP_DIR
-
Full path to the directory where temporary files will be stored.
- --with-petagene-dir WITH_PETAGENE_DIR
-
Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)
- --keep-tmp
-
Do not delete the directory storing temporary files after completion.
- --license-file LICENSE_FILE
-
Path to license file license.bin if not in the installation directory.
- --no-seccomp-override
-
Do not override seccomp options for docker (default: None).
- --version
-
View compatible software versions.
GPU options:
- --num-gpus NUM_GPUS
-
Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.
- --gpu-devices GPU_DEVICES
-
GPU devices to use for a run. By default, all GPU devices will be used. To use specific GPU devices, enter a comma-separated list of GPU device numbers. Possible device numbers can be found by examining the output of the
nvidia-smicommand. For example, using --gpu-devices 0,1 would only use the first two GPUs.