BioMonth - CSC supercomputing and data management for bioscientists

Deepvariant pipeline as developed by GoogleAI

Run deepvariant method to perform variant calling on WGS and WES data sets in Puhti supercomputing environment using deepvariant singularity container

How to get started

One needs the DeepVariant programs (https://github.com/google/deepvariant) and some test data. One can download data from Pouta object storage (or from google bucket) Storage.

Prepare deepvariant singulairty image from docker image

One needs to get deepvariant docker image, models and test data in order to run the pipeline. Additionally, other prerequisites for running deepvariant method includes 1) obtaining A reference genome in FASTA format and its corresponding index file (.fai). 2) An aligned reads file in BAM format and its corresponding index file (.bai).

Convert docker image to singularity

Log in to Puhti using your CSC credentials

Go to your subdirectory in the project scratch directory (created in last exercise):

cd /scratch/project_xxxx/$USER

Singularity is only available in compute nodes. We can use sinteractive to build the Singularity image in an interactive session.

sinteractive -i

Choose the course project. Set memory to 4 GB. You can use defaults for other parameters.

We want to use LOCAL_SCRATCH for Singularity tmp and cache. Unsetting XDG_RUNTIME_DIR will silence some unnecessary warnings.

export SINGULARITY_TMPDIR=$LOCAL_SCRATCH
export SINGULARITY_CACHEDIR=$LOCAL_SCRATCH
unset XDG_RUNTIME_DIR
singularity build deepvariant_cpu.sif docker://gcr.io/deepvariant-docker/deepvariant:0.8.0
exit

Copy test data

mkdir Deepvariant_singularity 
cp -fr /scratch/project_xxxx/Deepvariant_singularity/testdata  Deepvariant_singularity

Prepare slurm scripts to run on Puhti (e.g., deepvariant_puhti.sh)

#!/bin/bash
#SBATCH --time=00:05:00
#SBATCH --partition=small
#SBATCH --account=project_xxxx
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4000

mkdir -p tmp
export TMPDIR=$PWD/tmp

singularity exec --bind $PWD:$PWD --bind $PWD/tmp:/tmp --bind $PWD/Deepvariant_singularity/testdata:/testdata \
deepvariant_cpu.sif \
/opt/deepvariant/bin/run_deepvariant \
--model_type=WGS   --ref=/testdata/ucsc.hg19.chr20.unittest.fasta \
--reads=/testdata/NA12878_S1.chr20.10_10p1mb.bam \
--regions "chr20:10,000,000-10,010,000" \
--output_vcf=$PWD/output.vcf.gz \
--output_gvcf=$PWD/output.g.vcf.gz

Submit the job using sbatch command

sbatch  deepvariant_puhti.sh

Please note that one can use gpu version of deepvariant with the following sbatch script

#!/bin/bash
#SBATCH --time=00:05:00
#SBATCH --partition=gpu
#SBATCH --account=project_xxxx
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4000
#SBATCH --gres=gpu:v100:1

mkdir -p tmp
export TMPDIR=$PWD/tmp

singularity exec --nv --bind $PWD:$PWD --bind $PWD/tmp:/tmp --bind $PWD/Deepvariant_singularity/testdata:/testdata \
deepvariant_gpu.sif \
/opt/deepvariant/bin/run_deepvariant \
--model_type=WGS   --ref=/testdata/ucsc.hg19.chr20.unittest.fasta \
--reads=/testdata/NA12878_S1.chr20.10_10p1mb.bam \
--regions "chr20:10,000,000-10,010,000" \
--output_vcf=$PWD/output.vcf.gz \
--output_gvcf=$PWD/output.g.vcf.gz

This site is open source. Improve this page.