Post date: May 04, 2015 10:31:53 PM
#!/bin/sh
#PBS -N gatkUnifiedGenotyper
#PBS -l nodes=1:ppn=32
#PBS -l walltime=96:00:00
#PBS -l mem=960g
#PBS -q batch
. /rc/tools/utils/dkinit
reuse GATK
cd /home/A01963476/data/aspen/gbs/Assemblies/
java -jar -Xmx900g -Djava.io.tmpdir=/pscratch/A01963476/ /rc/tools/free/redhat_6_x86_64/gatk-3.1.1/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /labs/evolution/data/aspen/genome/Potrs01-genome.fa -I bams.list -o aspenvariants.vcf -nt 32 -glm SNP -hets 0.001 -mbq 20 -ploidy 2 -stand_call_conf 50 -maxAltAlleles 2