Pepper_deepvariant

Introduction

PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline. This pipeline enables nanopore-based variant calling with DeepVariant.

For more information, please check:

Docker hub: https://hub.docker.com/r/kishwars/pepper_deepvariant

Home page: https://github.com/kishwarshafin/pepper

Versions

• r0.4.1

Commands

• run_pepper_margin_deepvariant

Module

You can load the modules by:

module load biocontainers
module load pepper_deepvariant

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run pepper_deepvariant on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 32
#SBATCH --job-name=pepper_deepvariant
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pepper_deepvariant

BASE=$PWD

# 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=32

# 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

run_pepper_margin_deepvariant call_variant \
    -b input/data/HG002_ONT_2_GRCh38.chr20.quickstart.bam \
    -f input/data/GRCh38_no_alt.chr20.fa -o output \
    -p HG002_ONT_2_GRCh38_PEPPER_Margin_DeepVariant.chr20 \
    -t 32 -r chr20:1000000-1020000 \
    --ont_r9_guppy5_sup --ont