deepsomatic - NVIDIA Docs

GPU-accelerated DeepSomatic.

What is DeepSomatic?

DeepSomatic builds on the deep learning-based variant caller DeepVariant. It processes aligned reads from tumor and normal samples (in BAM or CRAM format), generates pileup image tensors, classifies these tensors using a convolutional neural network, and outputs somatic variants in standard VCF or gVCF files.

DeepSomatic is designed for somatic variant calling using tumor-normal sequencing data.

Parabricks has enhanced Google DeepSomatic to leverage GPUs extensively. The Parabricks version of DeepSomatic operates similarly to other common command line tools: it accepts two BAM files and a reference file as inputs and generates variants in a VCF file as output.

Quick Start

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            # This command assumes all the inputs are in INPUT_DIR and all the outputs go to OUTPUT_DIR.
docker run --rm --gpus all --volume INPUT_DIR:/workdir --volume OUTPUT_DIR:/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.3.1-1 \
    pbrun deepsomatic \
    --ref /workdir/${REFERENCE_FILE} \
    --in-tumor-bam /workdir/${INPUT_TUMOR_BAM} \
    --in-normal-bam /workdir/${INPUT_NORMAL_BAM} \
    --out-variants /outputdir/${OUTPUT_VCF}

Compatible Google DeepVariant Commands

The commands below are the Google counterpart of the Parabricks command above. The output from these commands will be identical to the output from the above command. See the Output Comparison page for comparing the results.

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            docker run \
--interactve \
--tty \
--rm \
--volume ${INPUT_DIR}:${INPUT_DIR} \
--volume ${OUTPUT_DIR}:${OUTPUT_DIR} \
--workdir /workdir google/deepvariant:1.6.1 \
run_deepsomatic \
--ref ${REFERENCE_FILE} \
--reads_tumor ${TUMOR_BAM} \
--reads_normal ${NORMAL_BAM}  \
--customized_model ${DEEPSOMATIC_WGS_MODEL_FILE} \
--output_vcf ${OUTPUT_VCF} \
--make_examples_extra_args "ws_use_window_selector_model=true" \
--num_shards=$(nproc)

deepsomatic Reference

Run DeepSomatic to convert BAM/CRAM to VCF.

Input/Output file options

--ref REF
--in-tumor-bam IN_TUMOR_BAM
--in-normal-bam IN_NORMAL_BAM
--interval-file INTERVAL_FILE
--out-variants OUT_VARIANTS
--pb-model-file PB_MODEL_FILE

Tool Options:

--disable-use-window-selector-model
--no-channel-insert-size
-L INTERVAL, --interval INTERVAL

Performance Options:

--num-cpu-threads-per-stream NUM_CPU_THREADS_PER_STREAM
--num-streams-per-gpu NUM_STREAMS_PER_GPU

Common options:

--logfile LOGFILE
--tmp-dir TMP_DIR
--with-petagene-dir WITH_PETAGENE_DIR
--keep-tmp
--no-seccomp-override
--version

GPU options:

--num-gpus NUM_GPUS