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# deepvariant_germline

Given one or more pairs of FASTQ files, you can run the germline variant
tool to generate BAM, variants, duplicate metrics and recal.

The deepvariant germline tool includes alignment, sorting, and marking as well as the
DeepVariant variant caller.

The inputs are BWA-indexed reference files and pair-ended FASTQ files. The outputs of this tool
are the following:

* Aligned, co-ordinate sorted, duplicated marked BAM

* Variants in `vcf`/`g.vcf`/`g.vcf.gz` format

![](/clara/parabricks/_files/parabricks-clara.docs.buildwithfern.com/f0988ccd6fda29b5800548b0db640342485714e519514ad0adc99978202d8f2a/assets/images/deep_variant.png)

Refer to the [deepvariant\_germline Reference](#options) section for a detailed listing of all available options.

## Quick Start

The following command runs the DeepVariant tool.

```sh
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
    pbrun deepvariant_germline \
    --ref /workdir/${REFERENCE_FILE} \
    --in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2} \
    --out-variants /outputdir/${OUTPUT_VCF_FILE} \
    --out-bam /outputdir/${OUTPUT_BAM_FILE}
```

## 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. Refer to the
[Output Comparison](/about-parabricks/comparison-with-baseline-tools) page for comparing the results.

```sh
# Run bwa-mem and pipe output to create sorted BAM
$ bwa mem \
    -t 32 \
    -K 10000000 \
    -R '@RG\tID:sample_rg1\tLB:lib1\tPL:bar\tSM:sample\tPU:sample_rg1' \
    <INPUT_DIR>/${REFERENCE_FILE} \
    <INPUT_DIR>/${INPUT_FASTQ_1} <INPUT_DIR>/${INPUT_FASTQ_2} | \
  gatk SortSam \
      --java-options -Xmx30g \
      --MAX_RECORDS_IN_RAM 5000000 \
      -I /dev/stdin \
      -O cpu.bam \
      --SORT_ORDER coordinate

# Mark Duplicates
$ gatk MarkDuplicates \
    --java-options -Xmx30g \
    -I cpu.bam \
    -O mark_dups_cpu.bam \
    -M metrics.txt

# Run deepvariant
BIN_VERSION="1.9.0"
sudo docker run \
  -v "${PWD}":"/input" \
  -v "${PWD}/output":"/output" \
  -v "${PWD}/Ref":"/reference" \
  google/deepvariant:"${BIN_VERSION}" \
  /opt/deepvariant/bin/run_deepvariant \
  --model_type WGS \
  --ref /reference/Homo_sapiens_assembly38.fasta \
  --reads /output/${OUTPUT_BAM_FILE} \
  --output_vcf /output/"${OUTPUT_VCF_FILE}" \
  --num_shards $(nproc) \
  --disable_small_model=true \
  --make_examples_extra_args "ws_use_window_selector_model=true"
```

In Google DeepVariant, the small model is enabled by default and must be explicitly disabled
(with `--disable_small_model=true`). In Parabricks DeepVariant, the small model is opt-in and
must be explicitly enabled (with `--enable-small-model`).

Variants called by the small model will have an additional `MID` field in their VCF record,
which denotes which model called the variant. This is consistent with VCF files produced by
Google DeepVariant.

## Models for Additional GPUs

See the DeepVariant [Models for additional GPUs](/tool-reference/tools/deepvariant#models-for-additional-gpus) section
for instructions on downloading and using model files for additional GPUs.

## Options

The *--in-fq* option takes the names of two FASTQ files, optionally followed by a
quoted read group.  The FASTQ filenames must not start with a hyphen.