Container for Training Parabricks DeepVariant

NVIDIA Clara Parabricks

Container

NVIDIA Clara Parabricks

Container for Training Parabricks DeepVariant

This container is used for running the data preprocessing part of DeepVariant Training pipeline including make_examples and shuffle

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This container is used for running the data preprocessing part of DeepVariant Training pipeline including make_examples and shuffle. It will generate output files 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:4.2.0-1 \
  pbrun make_examples --ref <REF_FILE> --reads <BAM_FILE> --truth-variants <TRUTH_VCF> --confident_regions <TRUTH_BED> \
  --examples <TFRECORD_FILE> --disable-use-window-selector-model --channel-insert-size \
  --num-gpus <GPU_NUM> --num-cpu-threads-per-stream <WORKER_THREAD_NUM> --num-zipper-threads <ZIPPER_THREAD_NUM>

This is a template command for running accelerated shuffle:

docker run --gpus all --rm -v <DATA_DIR>:<DATA_DIR> nvcr.io/nvidia/clara/deepvariant_train:4.2.0-1 \
  pbrun shuffle --input_pattern_list <INPUT_PATTERN_LIST> --output_pattern_prefix <OUTPUT_PATTERN_PREFIX> \
  --output_dataset_config <OUTPUT_PBTXT_FILE> --output_dataset_name <DATASET_NAME> --direct-num-workers <WORKER_THREAD_NUM>

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Publisher

NVIDIA Clara Parabricks

Latest Tag4.3.2-1

UpdatedSeptember 16, 2024 UTC

Compressed Size1.31 GB

Multinode SupportNo

Multi-Arch SupportNo

System

signed images

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