#!/bin/sh

#  VCFconvert.sh
#  
#
#  Created by Ramu Punna on 4/7/15.
#

perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr1.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr1.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr2.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr2.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr3.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr3.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr4.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr4.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr5.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr5.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr6.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr6.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr7.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr7.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr8.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr8.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr9.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr9.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr10.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr10.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr11.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr11.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr12.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr12.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr13.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr13.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr14.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr14.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr15.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr15.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr16.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr16.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr17.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr17.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr18.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr18.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr19.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr19.vcf -exportType VCF -runfork1
perl ./tasselNew/run_pipeline.pl -Xms64g -Xmx96g -fork1 -h5 ./genotypeFiles_HDF5format/igdBuildWithV6_hapmap_20150404_withRef_filter_chr20.h5 -export ./genotypeFiles_VCFformat/igdBuildWithV6_hapmap_20150404_withRef_filter_chr20.vcf -exportType VCF -runfork1
