#!/bin/sh

#  convertToVCFfiles.sh
#  
#
#  Created by Ramu Punna on 9/27/16.
#

perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr1.h5 -export danforthCenter_25Aug2017_withRef_chr1.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr2.h5 -export danforthCenter_25Aug2017_withRef_chr2.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr3.h5 -export danforthCenter_25Aug2017_withRef_chr3.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr4.h5 -export danforthCenter_25Aug2017_withRef_chr4.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr5.h5 -export danforthCenter_25Aug2017_withRef_chr5.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr6.h5 -export danforthCenter_25Aug2017_withRef_chr6.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr7.h5 -export danforthCenter_25Aug2017_withRef_chr7.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr8.h5 -export danforthCenter_25Aug2017_withRef_chr8.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr9.h5 -export danforthCenter_25Aug2017_withRef_chr9.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr10.h5 -export danforthCenter_25Aug2017_withRef_chr10.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr11.h5 -export danforthCenter_25Aug2017_withRef_chr11.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr12.h5 -export danforthCenter_25Aug2017_withRef_chr12.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr13.h5 -export danforthCenter_25Aug2017_withRef_chr13.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr14.h5 -export danforthCenter_25Aug2017_withRef_chr14.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr15.h5 -export danforthCenter_25Aug2017_withRef_chr15.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr16.h5 -export danforthCenter_25Aug2017_withRef_chr16.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr17.h5 -export danforthCenter_25Aug2017_withRef_chr17.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr18.h5 -export danforthCenter_25Aug2017_withRef_chr18.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr19.h5 -export danforthCenter_25Aug2017_withRef_chr19.vcf -exportType VCF -runfork1
perl ./tassel/run_pipeline.pl -Xms72g -Xmx96g -fork1 -h5 danforthCenter_25Aug2017_withRef_chr20.h5 -export danforthCenter_25Aug2017_withRef_chr20.vcf -exportType VCF -runfork1
