Table of Contents - cagnut_gatk-0.3.2 Documentation
Pages
Classes and Modules
- CagnutGatk
- CagnutGatk::AnalyzeCovariates
- CagnutGatk::Base
- CagnutGatk::BaseRecalibrator
- CagnutGatk::CheckTools
- CagnutGatk::Configuration
- CagnutGatk::CountRead
- CagnutGatk::DepthOfCoverage
- CagnutGatk::HaplotypeCaller
- CagnutGatk::IndelRealigner
- CagnutGatk::PrintReads
- CagnutGatk::RealignerTargetCreator
- CagnutGatk::UnifiedGenotyper
- CagnutGatk::Util
- CagnutGatk::VariantEval
- CagnutGatk::VariantFiltration
Methods
- ::config — CagnutGatk
- ::load — CagnutGatk::Configuration
- ::new — CagnutGatk::AnalyzeCovariates
- ::new — CagnutGatk::BaseRecalibrator
- ::new — CagnutGatk::CountRead
- ::new — CagnutGatk::DepthOfCoverage
- ::new — CagnutGatk::HaplotypeCaller
- ::new — CagnutGatk::IndelRealigner
- ::new — CagnutGatk::PrintReads
- ::new — CagnutGatk::RealignerTargetCreator
- ::new — CagnutGatk::UnifiedGenotyper
- ::new — CagnutGatk::VariantEval
- ::new — CagnutGatk::VariantFiltration
- ::new — CagnutGatk::Util
- #add_java_params — CagnutGatk::Configuration
- #analyze_covariates — CagnutGatk::Base
- #analyze_covariates — CagnutGatk::Util
- #analyze_covariates_options — CagnutGatk::AnalyzeCovariates
- #attributes — CagnutGatk::Configuration
- #base_recalibrator — CagnutGatk::Base
- #base_recalibrator — CagnutGatk::Util
- #base_recalibrator_options — CagnutGatk::BaseRecalibrator
- #before_and_after_generated_bqsr_file — CagnutGatk::Util
- #check_gatk — CagnutGatk::CheckTools
- #check_tool — CagnutGatk::CheckTools
- #cluster_options — CagnutGatk::AnalyzeCovariates
- #cluster_options — CagnutGatk::BaseRecalibrator
- #cluster_options — CagnutGatk::CountRead
- #cluster_options — CagnutGatk::DepthOfCoverage
- #cluster_options — CagnutGatk::HaplotypeCaller
- #cluster_options — CagnutGatk::IndelRealigner
- #cluster_options — CagnutGatk::PrintReads
- #cluster_options — CagnutGatk::RealignerTargetCreator
- #cluster_options — CagnutGatk::UnifiedGenotyper
- #cluster_options — CagnutGatk::VariantEval
- #cluster_options — CagnutGatk::VariantFiltration
- #count_read — CagnutGatk::Base
- #count_read — CagnutGatk::Util
- #count_read_params — CagnutGatk::Util
- #count_reads_options — CagnutGatk::CountRead
- #depth_of_coverage — CagnutGatk::Base
- #depth_of_coverage — CagnutGatk::Util
- #depth_of_coverage_options — CagnutGatk::DepthOfCoverage
- #depth_of_coverage_params — CagnutGatk::Util
- #file_basename — CagnutGatk::AnalyzeCovariates
- #file_basename — CagnutGatk::PrintReads
- #generate_script — CagnutGatk::AnalyzeCovariates
- #generate_script — CagnutGatk::BaseRecalibrator
- #generate_script — CagnutGatk::CountRead
- #generate_script — CagnutGatk::DepthOfCoverage
- #generate_script — CagnutGatk::HaplotypeCaller
- #generate_script — CagnutGatk::IndelRealigner
- #generate_script — CagnutGatk::PrintReads
- #generate_script — CagnutGatk::RealignerTargetCreator
- #generate_script — CagnutGatk::UnifiedGenotyper
- #generate_script — CagnutGatk::VariantEval
- #generate_script — CagnutGatk::VariantFiltration
- #haplotype_caller — CagnutGatk::Base
- #haplotype_caller — CagnutGatk::Util
- #haplotype_caller_options — CagnutGatk::HaplotypeCaller
- #indel_realigner — CagnutGatk::Base
- #indel_realigner — CagnutGatk::Util
- #indel_realigner_options — CagnutGatk::IndelRealigner
- #job_params — CagnutGatk::AnalyzeCovariates
- #job_params — CagnutGatk::BaseRecalibrator
- #job_params — CagnutGatk::CountRead
- #job_params — CagnutGatk::DepthOfCoverage
- #job_params — CagnutGatk::PrintReads
- #load — CagnutGatk::Configuration
- #modified_java_array — CagnutGatk::AnalyzeCovariates
- #modified_java_array — CagnutGatk::BaseRecalibrator
- #modified_java_array — CagnutGatk::CountRead
- #modified_java_array — CagnutGatk::DepthOfCoverage
- #modified_java_array — CagnutGatk::HaplotypeCaller
- #modified_java_array — CagnutGatk::IndelRealigner
- #modified_java_array — CagnutGatk::PrintReads
- #modified_java_array — CagnutGatk::RealignerTargetCreator
- #modified_java_array — CagnutGatk::UnifiedGenotyper
- #modified_java_array — CagnutGatk::VariantEval
- #modified_java_array — CagnutGatk::VariantFiltration
- #output_file — CagnutGatk::AnalyzeCovariates
- #output_file — CagnutGatk::PrintReads
- #params_combination — CagnutGatk::AnalyzeCovariates
- #params_combination — CagnutGatk::BaseRecalibrator
- #params_combination — CagnutGatk::CountRead
- #params_combination — CagnutGatk::HaplotypeCaller
- #params_combination — CagnutGatk::IndelRealigner
- #params_combination — CagnutGatk::PrintReads
- #params_combination — CagnutGatk::RealignerTargetCreator
- #params_combination — CagnutGatk::UnifiedGenotyper
- #params_combination — CagnutGatk::VariantEval
- #params_combination — CagnutGatk::VariantFiltration
- #params_combination_hash — CagnutGatk::DepthOfCoverage
- #print_reads — CagnutGatk::Base
- #print_reads — CagnutGatk::Util
- #print_reads_options — CagnutGatk::PrintReads
- #realigner_target_creator — CagnutGatk::Base
- #realigner_target_creator — CagnutGatk::Util
- #realigner_target_creator_options — CagnutGatk::RealignerTargetCreator
- #recal — CagnutGatk::Util
- #replace_filename — CagnutGatk::AnalyzeCovariates
- #replace_filename — CagnutGatk::PrintReads
- #run — CagnutGatk::AnalyzeCovariates
- #run — CagnutGatk::BaseRecalibrator
- #run — CagnutGatk::CountRead
- #run — CagnutGatk::DepthOfCoverage
- #run — CagnutGatk::HaplotypeCaller
- #run — CagnutGatk::IndelRealigner
- #run — CagnutGatk::PrintReads
- #run — CagnutGatk::RealignerTargetCreator
- #run — CagnutGatk::UnifiedGenotyper
- #run — CagnutGatk::VariantEval
- #run — CagnutGatk::VariantFiltration
- #setup_output_and_bqsr_file — CagnutGatk::BaseRecalibrator
- #snpcal — CagnutGatk::Util
- #unified_genotyper — CagnutGatk::Base
- #unified_genotyper — CagnutGatk::Util
- #unified_genotyper_options — CagnutGatk::UnifiedGenotyper
- #variant_eval — CagnutGatk::Base
- #variant_eval — CagnutGatk::Util
- #variant_eval_options — CagnutGatk::VariantEval
- #variant_filtration — CagnutGatk::Base
- #variant_filtration — CagnutGatk::Util
- #variant_filtration_options — CagnutGatk::VariantFiltration