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CatalogContainersContainer for Training DeepVariant

Container for Training DeepVariant

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Description

This container is used for running the data preprocessing part of DeepVariant Training pipeline called make examples

Publisher

NVIDIA Clara Parabricks

Latest Tag

4.1.0-1

Modified

June 1, 2023

Compressed Size

1.8 GB

Multinode Support

No

Multi-Arch Support

No

4.1.0-1 (Latest) Scan Results

Linux / amd64

This container is used for running the data preprocessing part of DeepVariant Training pipeline called make examples. It will generate outputs as tfrecord.gz which can be fed to DeepVariants model_train step.

This is a template command for running GPU accelerated make_examples:

docker run --gpus all --rm -v <DATA_DIR>:<DATA_DIR> nvcr.io/nvidia/clara/deepvariant_train:4.1.0-1 \
 /usr/local/parabricks/binaries/bin/deepvariant <REF_FILE> <BAM_FILE> <GPU_NUM> -o <OUTPUT_VCF> \
 -n <WORKER_THREAD_NUM> --channel_insert_size -L <REGIONS> -disable-use-window-selector-model \
--mode training --truth_variants <TRUTH_VCF> --confident_regions <TRUTH_BED> \
--examples <TFRECORD_FILE> -z <ZIPPER_THREAD_NUM>