mkdir test java -Xmx10g -jar /data/ngs/bin/GATK/3.3-0/GenomeAnalysisTK.jar -l INFO -K /data/ngs/bin/GATK/3.3-0/yong.li_uniklinik-freiburg.de.key -et NO_ET \ -T HaplotypeCaller \ -R /data/ngs/programs/bundle_2.8/ucsc.hg19.fasta \ -D /data/ngs/programs/bundle_2.8/dbsnp_138.hg19.vcf \ -L /data/ngs/exome_targets/SureSelect_V4_S03723314_Regions.bed \ -ERC GVCF \ -nct 4 \ -A Coverage \ -variant_index_type LINEAR \ -variant_index_parameter 128000 \ -I out/06-BQSR/21_428_1.bam \ -o test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-coverage.vcf \ -log test/08-variant-calling-noNCT/21_428_1/21_428_1-raw_calling-coverage.log & java -Xmx10g -jar /data/ngs/bin/GATK/3.3-0/GenomeAnalysisTK.jar -l INFO -K /data/ngs/bin/GATK/3.3-0/yong.li_uniklinik-freiburg.de.key -et NO_ET \ -T HaplotypeCaller \ -R /data/ngs/programs/bundle_2.8/ucsc.hg19.fasta \ -D /data/ngs/programs/bundle_2.8/dbsnp_138.hg19.vcf \ -L /data/ngs/exome_targets/SureSelect_V4_S03723314_Regions.bed \ -ERC GVCF \ -nct 4 \ -A AlleleBalance \ -variant_index_type LINEAR \ -variant_index_parameter 128000 \ -I out/06-BQSR/21_428_1.bam \ -o test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-AlleleBalance.vcf \ -log test/08-variant-calling-noNCT/21_428_1/21_428_1-raw_calling-AlleleBalance.log & java -Xmx10g -jar /data/ngs/bin/GATK/3.3-0/GenomeAnalysisTK.jar -l INFO -K /data/ngs/bin/GATK/3.3-0/yong.li_uniklinik-freiburg.de.key -et NO_ET \ -T HaplotypeCaller \ -R /data/ngs/programs/bundle_2.8/ucsc.hg19.fasta \ -D /data/ngs/programs/bundle_2.8/dbsnp_138.hg19.vcf \ -L /data/ngs/exome_targets/SureSelect_V4_S03723314_Regions.bed \ -ERC GVCF \ -nct 4 \ -A QualByDepth \ -variant_index_type LINEAR \ -variant_index_parameter 128000 \ -I out/06-BQSR/21_428_1.bam \ -o test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-QualByDepth.vcf \ -log test/08-variant-calling-noNCT/21_428_1/21_428_1-raw_calling-QualByDepth.log & java -Xmx10g -jar /data/ngs/bin/GATK/3.3-0/GenomeAnalysisTK.jar -l INFO -K /data/ngs/bin/GATK/3.3-0/yong.li_uniklinik-freiburg.de.key -et NO_ET \ -T HaplotypeCaller \ -R /data/ngs/programs/bundle_2.8/ucsc.hg19.fasta \ -D /data/ngs/programs/bundle_2.8/dbsnp_138.hg19.vcf \ -L /data/ngs/exome_targets/SureSelect_V4_S03723314_Regions.bed \ -ERC GVCF \ -nct 4 \ -A HaplotypeScore \ -variant_index_type LINEAR \ -variant_index_parameter 128000 \ -I out/06-BQSR/21_428_1.bam \ -o test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-HaplotypeScore.vcf \ -log test/08-variant-calling-noNCT/21_428_1/21_428_1-raw_calling-HaplotypeScore.log & java -Xmx10g -jar /data/ngs/bin/GATK/3.3-0/GenomeAnalysisTK.jar -l INFO -K /data/ngs/bin/GATK/3.3-0/yong.li_uniklinik-freiburg.de.key -et NO_ET \ -T HaplotypeCaller \ -R /data/ngs/programs/bundle_2.8/ucsc.hg19.fasta \ -D /data/ngs/programs/bundle_2.8/dbsnp_138.hg19.vcf \ -L /data/ngs/exome_targets/SureSelect_V4_S03723314_Regions.bed \ -ERC GVCF \ -nct 4 \ -variant_index_type LINEAR \ -variant_index_parameter 128000 \ -I out/06-BQSR/21_428_1.bam \ -o test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-all.vcf \ -log test/08-variant-calling-noNCT/21_428_1/21_428_1-raw_calling-all.log & wait Running GenotypeGVCF. java -Xmx10g -jar /data/ngs/bin/GATK/3.3-0/GenomeAnalysisTK.jar -l INFO -K /data/ngs/bin/GATK/3.3-0/yong.li_uniklinik-freiburg.de.key -et NO_ET \ -T GenotypeGVCFs \ -R /data/ngs/programs/bundle_2.8/ucsc.hg19.fasta \ -D /data/ngs/programs/bundle_2.8/dbsnp_138.hg19.vcf \ -stand_call_conf 30 \ -stand_emit_conf 30 \ -nt 12 \ -V test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-coverage.vcf \ -V test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-AlleleBalance.vcf \ -V test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-QualByDepth.vcf \ -V test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-HaplotypeScore.vcf \ -V test/08-variant-calling-noNCT/21_428_1/21_428_1-raw-all.vcf \ -o test/08-variant-calling-noNCT/combined/combined_raw.vcf \ -log test/08-variant-calling-noNCT/GenotypeGVCF.log