Container for Training DeepVariant

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>