Simplified DeepVariant singularity wrappers for small PacBio datasets

00_README.md

Simplified DeepVariant singularity wrappers for small PacBio datasets

Adapted from DeepVariant documentation.

CPU-only

# pull docker image (only need to do this once)
BIN_VERSION=0.10.0
singularity pull docker://google/deepvariant:"${BIN_VERSION}"

# run DeepVariant
REF=/path/to/reference.fasta INPUT=ccs.bam bash run_deepvariant.sh

GPU accelerated calling

# pull docker image (only need to do this once)
BIN_VERSION=0.10.0-gpu
singularity pull docker://google/deepvariant:"${BIN_VERSION}"

# run DeepVariant
REF=/path/to/reference.fasta INPUT=ccs.bam bash run_deepvariant_gpu.sh

run_deepvariant.sh

#!/bin/bash

set -x

BIN_VERSION=0.10.0
OUTPUTDIR=${PWD}/${OUTPUT:-deepvariant}
mkdir "${OUTPUTDIR}"
# BIN_VERSION=0.10.0
# singularity pull docker://google/deepvariant:"${BIN_VERSION}"

time singularity exec --bind $PWD,/scratch:/tmp,/usr/lib/locale/,${REF%/*} \
  docker://google/deepvariant:"${BIN_VERSION}" \
    /opt/deepvariant/bin/run_deepvariant \
    --model_type PACBIO \
    --ref "${REF}" \
    --reads "${INPUT}" \
    --output_vcf "${OUTPUTDIR}/output.vcf.gz" \
    --num_shards $(nproc)

set +x

run_deepvariant_gpu.sh

#!/bin/bash

set -x

CUDA_VISIBLE_DEVICES=0  # run on first device
BIN_VERSION=0.10.0-gpu
OUTPUTDIR=${PWD}/${OUTPUT:-deepvariant}
mkdir "${OUTPUTDIR}"
# BIN_VERSION=0.10.0-gpu
# singularity pull docker://google/deepvariant:"${BIN_VERSION}"

time singularity exec --nv --bind $PWD,/scratch:/tmp,/usr/lib/locale/,${REF%/*} \
  docker://google/deepvariant:"${BIN_VERSION}" \
    /opt/deepvariant/bin/run_deepvariant \
    --model_type PACBIO \
    --ref "${REF}" \
    --reads "${INPUT}" \
    --output_vcf "${OUTPUTDIR}/output.vcf.gz" \
    --num_shards $(nproc)

set +x