gatk4_gathervcfs.sh

#!/bin/bash

#########################################################
# 
# Platform: NCI Gadi HPC 
# Usage: 
# Version: 2.0 
# 
# For more details see: https://github.com/Sydney-Informatics-Hub/Germline-ShortV 
# 
# If you use this script towards a publication, support us by citing: 
# 
# Suggest citation: 
# Sydney Informatics Hub, Core Research Facilities, University of Sydney, 
# 2021, The Sydney Informatics Hub Bioinformatics Repository, <date accessed>, 
# https://github.com/Sydney-Informatics-Hub/Germline-ShortV 
# 
# Please acknowledge the Sydney Informatics Hub and the facilities: 
# 
# Suggested acknowledgement: 
# The authors acknowledge the technical assistance provided by the Sydney 
# Informatics Hub, a Core Research Facility of the University of Sydney 
# and the Australian BioCommons which is enabled by NCRIS via Bioplatforms 
# Australia. The authors acknowledge the use of the National Computational 
# Infrastructure (NCI) supported by the Australian Government. 
# 
#########################################################

set -e

sample=`echo $1 | cut -d ',' -f 1`
args=`echo $1 | cut -d ',' -f 2`
logdir=`echo $1 | cut -d ',' -f 3`
out=`echo $1 | cut -d ',' -f 4`
errdir=`echo $1 | cut -d ',' -f 5`

logfile=${logdir}/${sample}.log
errfile=${errdir}/${sample}.err

mkdir -p ${logdir}
rm -rf ${errfile}

gatk GatherVcfs --java-options "-Xmx16g -XX:ParallelGCThreads=${NCPUS} -Djava.io.tmpdir=${PBS_JOBFS}" \
	--arguments_file ${args} \
	--MAX_RECORDS_IN_RAM 1000000000 \
	-O ${out} > ${logfile} 2>&1

# Check logs for GATK errors
if grep -q -i error $log
then
        printf "Error in GATK log ${log}\n" >> $err
fi

if grep -q Exception $log
then
        printf "Exception in GATK log ${log}\n" >> $err
fi