GATK4

#!/bin/bash -x
#PBS -N GATK4
#PBS -q batch


### Switch to the working directory; by default TORQUE launches processes from your home directory.
cd $PBS_O_WORKDIR
echo Working directory is $PBS_O_WORKDIR


module load java/java-1.8.0
module load bio/samtools-1.9

export INPATH=/mnt/home/usr/infiles
export OUTPATH=/home/usr/outfiles
mkdir -p $OUTPATH
chmod u+rwx $OUTPATH
export reference=/mnt/home/usr/references/refseq.fasta

java -jar /mnt/home/usr/tools/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar CreateSequenceDictionary -R $reference
samtools faidx $reference
for file in $INPATH/*.bam  ;
do
        bname=$(basename $file ".bam")
        echo $bname
        variants=$OUTPATH/$bname".vcf"
        echo $variants
        samtools index $file

         java -Xmx4G -jar /mnt/home/usr/tools/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar HaplotypeCaller \
        -R $reference \
        -ploidy 1 \
        -I $file \
        -O $variants \
         -ERC GVCF \
        --read-filter OverclippedReadFilter \
        --QUIET \

done