Here we show a quickstart for using Docker in your system.
Expand to see docker installation guide.
Please install docker and wget if you don't have it installed already. You can install docker for other distros from here:
- CentOS docker installation guide
- Debian/Raspbian docker installation guide
- Fedora installation guide
- Ubuntu installation guide
We show the installation instructions for Ubuntu here:
# Install wget to download data files.
sudo apt-get -qq -y update
sudo apt-get -qq -y install wget
# Install docker using instructions on:
# https://docs.docker.com/install/linux/docker-ce/ubuntu/
sudo apt-get -qq -y install apt-transport-https ca-certificates curl gnupg-agent software-properties-common
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository \
"deb [arch=amd64] https://download.docker.com/linux/ubuntu \
$(lsb_release -cs) \
stable"
sudo apt-get -qq -y update
sudo apt-get -qq -y install docker-ce
docker --version
# To add the user to avoid running docker with sudo:
# Details: https://docs.docker.com/engine/install/linux-postinstall/
sudo groupadd docker
sudo usermod -aG docker $USER
# Log out and log back in so that your group membership is re-evaluated.
# After logging back in.
docker run hello-world
# If you can run docker without sudo then change the following commands accordingly.BASE="${HOME}/docker-quickstart"
# Set up input data
INPUT_DIR="${BASE}/input/data"
REF="GRCh38_no_alt.chr20.fa"
BAM="HG002_ONT_2_GRCh38.chr20.quickstart.bam"
# Set the number of CPUs to use
THREADS="1"
# Set up output directory
OUTPUT_DIR="${BASE}/output"
OUTPUT_PREFIX="HG002_ONT_2_GRCh38_PEPPER_Margin_DeepVariant.chr20"
OUTPUT_VCF="HG002_ONT_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.vcf.gz"
TRUTH_VCF="HG002_GRCh38_1_22_v4.2.1_benchmark.quickstart.vcf.gz"
TRUTH_BED="HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.quickstart.bed"
## Create local directory structure
mkdir -p "${OUTPUT_DIR}"
mkdir -p "${INPUT_DIR}"
# Download the data to input directory
wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/quickstart_data/HG002_ONT_2_GRCh38.chr20.quickstart.bam
wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/quickstart_data/HG002_ONT_2_GRCh38.chr20.quickstart.bam.bai
wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/quickstart_data/GRCh38_no_alt.chr20.fa
wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/quickstart_data/GRCh38_no_alt.chr20.fa.fai
wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/quickstart_data/HG002_GRCh38_1_22_v4.2.1_benchmark.quickstart.vcf.gz
wget -P ${INPUT_DIR} https://storage.googleapis.com/pepper-deepvariant-public/quickstart_data/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.quickstart.bed
# Pull the docker images
sudo docker pull jmcdani20/hap.py:v0.3.12
sudo docker pull kishwars/pepper_deepvariant:r0.8
# Run PEPPER-Margin-DeepVariant
sudo docker run \
-v "${INPUT_DIR}":"${INPUT_DIR}" \
-v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
kishwars/pepper_deepvariant:r0.8 \
run_pepper_margin_deepvariant call_variant \
-b "${INPUT_DIR}/${BAM}" \
-f "${INPUT_DIR}/${REF}" \
-o "${OUTPUT_DIR}" \
-p "${OUTPUT_PREFIX}" \
-t ${THREADS} \
-r chr20:1000000-1020000 \
--ont_r9_guppy5_sup
# Run hap.py
sudo docker run -it \
-v "${INPUT_DIR}":"${INPUT_DIR}" \
-v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
${INPUT_DIR}/${TRUTH_VCF} \
${OUTPUT_DIR}/${OUTPUT_VCF} \
-f "${INPUT_DIR}/${TRUTH_BED}" \
-r "${INPUT_DIR}/${REF}" \
-o "${OUTPUT_DIR}/happy.output" \
--pass-only \
-l chr20:1000000-1020000 \
--engine=vcfeval \
--threads="${THREADS}"Expected output:
| Type | Truth total |
True positives |
False negatives |
False positives |
Recall | Precision | F1-Score |
|---|---|---|---|---|---|---|---|
| INDEL | 2 | 2 | 0 | 0 | 1.0 | 1.0 | 1.0 |
| SNP | 39 | 39 | 39 | 39 | 1.0 | 1.0 | 1.0 |
This pipeline is developed in a collaboration between UCSC genomics institute and the genomics team at Google health.