gatk4-exome-analysis-pipeline

Purpose :

This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

Requirements/expectations :

• Human exome sequencing data in unmapped BAM (uBAM) format
• One or more read groups, one per uBAM file, all belonging to a single sample (SM)
• Input uBAM files must additionally comply with the following requirements:
• • filenames all have the same suffix (we use ".unmapped.bam")
• • files must pass validation by ValidateSamFile
• • reads are provided in query-sorted order
• • all reads must have an RG tag
• GVCF output names must end in ".g.vcf.gz"
• Reference genome must be Hg38 with ALT contigs
• Unique exome calling, target, and bait .interval_list obtained from sequencing provider. Generally the calling, target, and bait files will not be the same.

Output :

• Cram, cram index, and cram md5
• GVCF and its gvcf index
• BQSR Report
• Several Summary Metrics

Installing the workflow and cromwell

git clone --recursive https://github.com/MonashBioinformaticsPlatform/gatk4-exome-analysis-pipeline.git
# Create a conda environment called 'cromwell', and install cromwell into it
conda create -n cromwell -c bioconda -c conda-forge cromwell
conda activate cromwell
pip install gsutil
pip install j2cli

Getting the references and example data

export REF_BASE=/scratch/pl41/references
mkdir -p $REF_BASE/references/broad-references/
cd $REF_BASE/references/broad-references/
gsutil -m rsync -r -x "CrossSpeciesContamination/*" gs://broad-references/hg38 hg38

mkdir -p $REF_BASE/references/gatk-best-practices/exome-analysis-pipeline
cd $REF_BASE/references/gatk-best-practices/exome-analysis-pipeline
gsutil -m cp gs://gatk-best-practices/exome-analysis-pipeline/SRR099969.unmapped.bam SRR099969.unmapped.bam .
# wget https://storage.googleapis.com/gatk-best-practices/exome-analysis-pipeline/SRR099969.unmapped.bam

Running (example)

Generate inputs.json and options.json files based on the template:

export REF_BASE=/scratch/pl41/references
export SLURM_ACCOUNT=pl41
export SINGULARITY_CACHE=/scratch/${SLURM_ACCOUNT}/singularity_cache
export SINGULARITY_BIND_PATH=/scratch
export TMPDIR=/scratch/${SLURM_ACCOUNT}/tmp

j2 gatk4-exome-analysis-pipeline/ExomeGermlineSingleSample.inputs.json.j2 \
   >gatk4-exome-analysis-pipeline/ExomeGermlineSingleSample.inputs.json

j2 gatk4-exome-analysis-pipeline/ExomeGermlineSingleSample.options.json.j2 \
   >gatk4-exome-analysis-pipeline/ExomeGermlineSingleSample.options.json

Run the pipeline:

cromwell -Xmx8g \
         -Dconfig.file=$(pwd)/gatk4-exome-analysis-pipeline/slurm-backend.conf \
         -Dsystem.input-read-limits.lines=1000000 \
         -Ddefault_runtime_attributes.tmp=$TMPDIR \
         -Ddefault_runtime_attributes.singularity_cache=$SINGULARITY_CACHE \
         -Ddefault_runtime_attributes.singularity_bind_path=$SINGULARITY_BIND_PATH \
         -Ddefault_runtime_attributes.slurm_account=$SLURM_ACCOUNT \
         run gatk4-exome-analysis-pipeline/ExomeGermlineSingleSample.wdl \
         --inputs gatk4-exome-analysis-pipeline/ExomeGermlineSingleSample.inputs.json \
         --options gatk4-exome-analysis-pipeline/ExomeGermlineSingleSample.options.json

Software version notes :

• GATK 4 or later
• Cromwell version support
  • Successfully tested on v36
  • Does not work on versions < v23 due to output syntax

Important Note :

• Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
• For help running workflows on the Google Cloud Platform or locally please view the following tutorial (How to) Execute Workflows from the gatk-workflows Git Organization.
• The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : GATK , FireCloud , WDL/Cromwell.
• Please visit the User Guide site for further documentation on our workflows and tools.

LICENSING :

Copyright Broad Institute, 2018 | BSD-3

This script is released under the WDL open source code license (BSD-3) (full license text at https://github.com/openwdl/wdl/blob/master/LICENSE). Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script.