Method List
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#add_java_params CagnutGatk::Configuration
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#analyze_covariates CagnutGatk::Base
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#analyze_covariates CagnutGatk::Util
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#analyze_covariates_options CagnutGatk::AnalyzeCovariates
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#analyze_covariates_params CagnutGatk::Configuration
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#attributes CagnutGatk::Configuration
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#base_recalibrator CagnutGatk::Base
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#base_recalibrator CagnutGatk::Util
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#base_recalibrator_options CagnutGatk::BaseRecalibrator
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#base_recalibrator_params CagnutGatk::Configuration
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#check_gatk CagnutGatk::CheckTools
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#check_tool CagnutGatk::CheckTools
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#cluster_options CagnutGatk::IndelRealigner
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#cluster_options CagnutGatk::BaseRecalibrator
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#cluster_options CagnutGatk::VariantEval
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#cluster_options CagnutGatk::AnalyzeCovariates
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#cluster_options CagnutGatk::DepthOfCoverage
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#cluster_options CagnutGatk::CountRead
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#cluster_options CagnutGatk::VariantFiltration
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#cluster_options CagnutGatk::RealignerTargetCreator
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#cluster_options CagnutGatk::UnifiedGenotyper
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#cluster_options CagnutGatk::HaplotypeCaller
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#cluster_options CagnutGatk::PrintReads
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#config CagnutGatk::Util
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config CagnutGatk
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#count_read CagnutGatk::Util
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#count_read CagnutGatk::Base
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#count_reads_options CagnutGatk::CountRead
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#count_reads_params CagnutGatk::Configuration
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#depth_of_coverage CagnutGatk::Util
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#depth_of_coverage CagnutGatk::Base
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#depth_of_coverage_options CagnutGatk::DepthOfCoverage
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#depth_of_coverage_params CagnutGatk::Configuration
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#file_basename CagnutGatk::AnalyzeCovariates
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#file_basename CagnutGatk::PrintReads
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#gatk CagnutGatk::Util
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#generate_script CagnutGatk::PrintReads
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#generate_script CagnutGatk::VariantFiltration
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#generate_script CagnutGatk::VariantEval
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#generate_script CagnutGatk::UnifiedGenotyper
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#generate_script CagnutGatk::RealignerTargetCreator
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#generate_script CagnutGatk::AnalyzeCovariates
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#generate_script CagnutGatk::DepthOfCoverage
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#generate_script CagnutGatk::HaplotypeCaller
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#generate_script CagnutGatk::IndelRealigner
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#generate_script CagnutGatk::CountRead
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#generate_script CagnutGatk::BaseRecalibrator
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#haplotype_caller CagnutGatk::Util
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#haplotype_caller CagnutGatk::Base
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#haplotype_caller_options CagnutGatk::HaplotypeCaller
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#haplotype_caller_params CagnutGatk::Configuration
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#indel_realigner CagnutGatk::Util
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#indel_realigner CagnutGatk::Base
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#indel_realigner_options CagnutGatk::IndelRealigner
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#indel_realigner_params CagnutGatk::Configuration
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#initialize CagnutGatk::IndelRealigner
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#initialize CagnutGatk::RealignerTargetCreator
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#initialize CagnutGatk::AnalyzeCovariates
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#initialize CagnutGatk::HaplotypeCaller
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#initialize CagnutGatk::Util
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#initialize CagnutGatk::UnifiedGenotyper
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#initialize CagnutGatk::PrintReads
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#initialize CagnutGatk::VariantEval
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#initialize CagnutGatk::VariantFiltration
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#initialize CagnutGatk::BaseRecalibrator
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#initialize CagnutGatk::CountRead
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#initialize CagnutGatk::DepthOfCoverage
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#job_params CagnutGatk::PrintReads
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#job_params CagnutGatk::CountRead
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#job_params CagnutGatk::AnalyzeCovariates
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#job_params CagnutGatk::DepthOfCoverage
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#job_params CagnutGatk::BaseRecalibrator
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#load CagnutGatk::Configuration
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load CagnutGatk::Configuration
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#modified_java_array CagnutGatk::PrintReads
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#modified_java_array CagnutGatk::HaplotypeCaller
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#modified_java_array CagnutGatk::CountRead
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#modified_java_array CagnutGatk::AnalyzeCovariates
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#modified_java_array CagnutGatk::UnifiedGenotyper
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#modified_java_array CagnutGatk::VariantFiltration
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#modified_java_array CagnutGatk::RealignerTargetCreator
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#modified_java_array CagnutGatk::DepthOfCoverage
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#modified_java_array CagnutGatk::BaseRecalibrator
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#modified_java_array CagnutGatk::VariantEval
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#modified_java_array CagnutGatk::IndelRealigner
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#output_file CagnutGatk::PrintReads
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#output_file CagnutGatk::AnalyzeCovariates
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#params_combination CagnutGatk::PrintReads
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#params_combination CagnutGatk::CountRead
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#params_combination CagnutGatk::AnalyzeCovariates
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#params_combination CagnutGatk::RealignerTargetCreator
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#params_combination CagnutGatk::VariantFiltration
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#params_combination CagnutGatk::BaseRecalibrator
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#params_combination CagnutGatk::UnifiedGenotyper
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#params_combination CagnutGatk::HaplotypeCaller
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#params_combination CagnutGatk::IndelRealigner
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#params_combination CagnutGatk::VariantEval
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#params_combination_hash CagnutGatk::DepthOfCoverage
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#print_reads CagnutGatk::Util
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#print_reads CagnutGatk::Base
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#print_reads_options CagnutGatk::PrintReads
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#print_reads_params CagnutGatk::Configuration
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#realigner_target_creator CagnutGatk::Util
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#realigner_target_creator CagnutGatk::Base
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#realigner_target_creator_options CagnutGatk::RealignerTargetCreator
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#realigner_target_creator_params CagnutGatk::Configuration
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#recal CagnutGatk::Util
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#replace_filename CagnutGatk::PrintReads
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#replace_filename CagnutGatk::AnalyzeCovariates
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#run CagnutGatk::UnifiedGenotyper
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#run CagnutGatk::DepthOfCoverage
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#run CagnutGatk::BaseRecalibrator
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#run CagnutGatk::HaplotypeCaller
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#run CagnutGatk::IndelRealigner
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#run CagnutGatk::VariantFiltration
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#run CagnutGatk::PrintReads
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#run CagnutGatk::CountRead
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#run CagnutGatk::VariantEval
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#run CagnutGatk::RealignerTargetCreator
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#run CagnutGatk::AnalyzeCovariates
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#setup_output_and_bqsr_file CagnutGatk::BaseRecalibrator
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#snpcal CagnutGatk::Util
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#unified_genotyper CagnutGatk::Base
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#unified_genotyper CagnutGatk::Util
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#unified_genotyper_options CagnutGatk::UnifiedGenotyper
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#unified_genotyper_params CagnutGatk::Configuration
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#variant_eval CagnutGatk::Util
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#variant_eval CagnutGatk::Base
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#variant_eval_options CagnutGatk::VariantEval
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#variant_eval_params CagnutGatk::Configuration
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#variant_filtration CagnutGatk::Util
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#variant_filtration CagnutGatk::Base
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#variant_filtration_options CagnutGatk::VariantFiltration
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#variant_filtration_params CagnutGatk::Configuration