/usr/bin/time -v /data/Udpbinfo/WES/DiploidAlign/bin//gatk.sh 50 /data/Udpbinfo/WES/DiploidAlign/118Cohort//ITERATION_0/118Cohort.SNPChipIT0IT1.combined.dupsremoved.part1of4.vcf.HC.TomPEDFilev4.ITERATION_0.vcf.gc.log -T HaplotypeCaller -R /data/Udpbinfo/WES/DiploidAlign/GATK-Resources/hs37d5.fa -nct 14 -ped /data/Udpbinfo/WES/DiploidAlign/inputFiles/TomPEDFilev4.ped -I /data/Udpbinfo/WES/DiploidAlign/GenotypeCalls/HaplotypePrep/BAMSForGenotyping.it0.list -dcov 200 -minPruning 4 -o /data/Udpbinfo/WES/DiploidAlign/118Cohort//ITERATION_0/118Cohort.SNPChipIT0IT1.combined.dupsremoved.part1of4.vcf.HC.TomPEDFilev4.ITERATION_0.vcf -L /data/Udpbinfo/WES/DiploidAlign/118Cohort/118Cohort.SNPChipIT0IT1.combined.dupsremoved.part1of4.vcf -stand_emit_conf 0 -out_mode EMIT_ALL_SITES --dbsnp /data/Udpbinfo/WES/DiploidAlign/GATK-Resources/dbsnp_137.b37.vcf > /data/Udpbinfo/WES/DiploidAlign/118Cohort//ITERATION_0/118Cohort.SNPChipIT0IT1.combined.dupsremoved.part1of4.vcf.HC.TomPEDFilev4.ITERATION_0.vcf.stdout 2> /data/Udpbinfo/WES/DiploidAlign/118Cohort//ITERATION_0/118Cohort.SNPChipIT0IT1.combined.dupsremoved.part1of4.vcf.HC.TomPEDFilev4.ITERATION_0.vcf.stderr ; echo $? > /data/Udpbinfo/WES/DiploidAlign/118Cohort//ITERATION_0/118Cohort.SNPChipIT0IT1.combined.dupsremoved.part1of4.vcf.HC.TomPEDFilev4.ITERATION_0.vcf.exit