Difference between revisions of "UGP Pipeline Config Template 0.0.4"
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(Created page with "<pre> ############################################################# ############################################################# ################## cApTUrE config file #####...") |
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<pre> | <pre> | ||
+ | |||
############################################################# | ############################################################# | ||
############################################################# | ############################################################# | ||
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## The sample name and lane information of the fastq file are the most important parts for the pipeline to work correctly. | ## The sample name and lane information of the fastq file are the most important parts for the pipeline to work correctly. | ||
## Boolean options must be specified as TRUE (false values as blanks). | ## Boolean options must be specified as TRUE (false values as blanks). | ||
+ | |||
[required] | [required] | ||
# ugp_id is a unique identifier for each project in the format UGP_0001 | # ugp_id is a unique identifier for each project in the format UGP_0001 | ||
− | ugp_id | + | ugp_id: UGP_0001 |
# ugp_verson describes the version of the pipeline used | # ugp_verson describes the version of the pipeline used | ||
− | ugp_version : 0.0.2 | + | ugp_version: 0.0.2 |
# location of md5 file to check data integrity | # location of md5 file to check data integrity | ||
− | md5 | + | md5: /home/srynearson/cApTUrE/Fastq/<FILE> |
− | # The path to the reference genome fasta file ( | + | # The path to the reference genome fasta file (include file) |
− | fasta | + | fasta: /home/srynearson/cAPTUrE/references/human_g1k_v37.fasta |
# The path to the project fastq files. | # The path to the project fastq files. | ||
# include trailing slash! | # include trailing slash! | ||
− | fastq_dir | + | fastq_dir: /data/srynearson/Fastq/ |
# The name of the command line and pipeline info log file | # The name of the command line and pipeline info log file | ||
− | command_log | + | command_log: cmd.log |
− | # The number of CPUs available for Perl to parallel process | + | # The number of CPUs available for Perl to parallel process |
− | cpu | + | # Matching to number of fastq file works best |
+ | cpu: 8 | ||
− | # The Xmx (memory usage) for | + | # The Xmx (memory usage) for Picard tools |
− | picard_java_Xmx : | + | # max shoud be set to 125 |
+ | picard_java_Xmx: 50 | ||
# The Xmx (memory usage) for GATK RealignerTargetCreator | # The Xmx (memory usage) for GATK RealignerTargetCreator | ||
− | gatk_tc_Xmx : | + | gatk_tc_Xmx: 125 |
# The Xmx (memory usage) for GATK IndelRealigner | # The Xmx (memory usage) for GATK IndelRealigner | ||
− | gatk_ir_Xmx : 125 | + | gatk_ir_Xmx: 125 |
# The Xmx (memory usage) for GATK BaseRecalibrator | # The Xmx (memory usage) for GATK BaseRecalibrator | ||
− | gatk_br_Xmx : 125 | + | gatk_br_Xmx: 125 |
# The Xmx (memory usage) for PrintReads | # The Xmx (memory usage) for PrintReads | ||
− | gatk_pr_Xmx : 125 | + | gatk_pr_Xmx: 125 |
# The Xmx (memory usage) for ReduceReads | # The Xmx (memory usage) for ReduceReads | ||
− | gatk_rr_Xmx : 125 | + | gatk_rr_Xmx: 125 |
# The Xmx (memory usage) for UnifiedGenotyper | # The Xmx (memory usage) for UnifiedGenotyper | ||
− | gatk_ug_Xmx : | + | gatk_ug_Xmx: 125 |
− | # The path to temp | + | # The path to temp dir used by java |
− | java_tmp | + | java_tmp: /tmp/ |
# Path to VCF files for RealignerTargetCreator knowns | # Path to VCF files for RealignerTargetCreator knowns | ||
− | known_indel : /home/srynearson/cAPTUrE/background_files/known_indels | + | known_indel: /home/srynearson/cAPTUrE/background_files/known_indels |
− | known_dbSNP : /home/srynearson/cAPTUrE/background_files/known_dbSNP | + | known_dbSNP: /home/srynearson/cAPTUrE/background_files/known_dbSNP |
# Path to background bams used running UnifiedGenotyper | # Path to background bams used running UnifiedGenotyper | ||
# not required to run but will improve variant calls | # not required to run but will improve variant calls | ||
− | unified_bg_bams : /data/srynearson/reducedreads/ | + | unified_bg_bams: /data/srynearson/reducedreads/ |
# Resource files (including path) for VariantRecalibrator_SNP | # Resource files (including path) for VariantRecalibrator_SNP | ||
Line 71: | Line 75: | ||
vqsr_snp_vcf: /data/srynearson/resources/hapmap_3.3.b37.vcf | vqsr_snp_vcf: /data/srynearson/resources/hapmap_3.3.b37.vcf | ||
vqsr_snp_vcf: /data/srynearson/resources/1000G_omni2.5.b37.vcf | vqsr_snp_vcf: /data/srynearson/resources/1000G_omni2.5.b37.vcf | ||
− | vqsr_snp_vcf: /data/srynearson/resources/1000G_phase1.snps.high_confidence.b37.vcf | + | vqsr_snp_vcf: /data/srynearson/resources/1000G_phase1.snps.high_confidence.b37.vcf |
# Resource files (including path) for VariantRecalibrator_INDEL | # Resource files (including path) for VariantRecalibrator_INDEL | ||
# Order must match VariantRecalibrator_INDEL option below! | # Order must match VariantRecalibrator_INDEL option below! | ||
− | vsqr_indel_vcf : /data/srynearson/resources/Mills_and_1000G_gold_standard.indels.b37.vcf | + | vsqr_indel_vcf: /data/srynearson/resources/Mills_and_1000G_gold_standard.indels.b37.vcf |
− | vsqr_indel_vcf : /data/srynearson/resources/dbsnp_137.b37.vcf | + | vsqr_indel_vcf: /data/srynearson/resources/dbsnp_137.b37.vcf |
# path to needed software(required). | # path to needed software(required). | ||
[software] | [software] | ||
− | bwa | + | bwa: /usr/local/bwa/ |
− | fastqc | + | fastqc: /usr/local/FastQC/ |
− | picard | + | picard: /usr/local/picard-tools/ |
− | samtools : /usr/local/samtools/ | + | samtools: /usr/local/samtools/ |
− | gatk | + | gatk: /usr/local/GenomeAnalysisTK-2.7-2/GenomeAnalysisTK.jar |
− | |||
− | |||
+ | # Pipeline Run Order. | ||
[order] | [order] | ||
− | ## requires at least two commands be used | + | ## requires at least two commands to be used |
#command_order : indexer | #command_order : indexer | ||
− | + | command_order: fastqc | |
− | command_order : bwa_aln | + | command_order: bwa_aln |
− | command_order : bwa_sampe | + | command_order: bwa_sampe |
− | command_order : idxstats | + | command_order: idxstats |
− | command_order : flagstat | + | command_order: flagstat |
− | command_order : MergeSamFiles | + | command_order: MergeSamFiles |
− | command_order : MarkDuplicates | + | command_order: MarkDuplicates |
− | command_order : RealignerTargetCreator | + | command_order: RealignerTargetCreator |
− | command_order : IndelRealigner | + | command_order: IndelRealigner |
− | command_order : BaseRecalibrator | + | command_order: BaseRecalibrator |
− | command_order : PrintReads | + | command_order: PrintReads |
− | command_order : CollectMultipleMetrics | + | command_order: CollectMultipleMetrics |
− | command_order : ReduceReads | + | command_order: ReduceReads |
− | command_order : UnifiedGenotyper | + | command_order: UnifiedGenotyper |
− | command_order : VariantRecalibrator | + | command_order: VariantRecalibrator |
− | command_order : ApplyRecalibration | + | command_order: ApplyRecalibration |
# VariantRecalibrator will run both SNP and INDEL version | # VariantRecalibrator will run both SNP and INDEL version | ||
− | # | + | # can be ran independently if desired. |
#command_order : VariantRecalibrator_SNP | #command_order : VariantRecalibrator_SNP | ||
#command_order : VariantRecalibrator_INDEL | #command_order : VariantRecalibrator_INDEL | ||
#command_order : ApplyRecalibration_SNP | #command_order : ApplyRecalibration_SNP | ||
#command_order : ApplyRecalibration_INDEL | #command_order : ApplyRecalibration_INDEL | ||
− | |||
######################### FASTQC ############################ | ######################### FASTQC ############################ | ||
Line 121: | Line 123: | ||
[fastqc] | [fastqc] | ||
− | outdir | + | outdir: |
− | extract : | + | extract: |
− | threads : | + | threads: 10 |
− | kmers | + | kmers: |
− | quiet | + | quiet: |
######################### BWA ############################### | ######################### BWA ############################### | ||
Line 132: | Line 134: | ||
[bwa_index] | [bwa_index] | ||
− | p : | + | p: |
− | a : bwtsw | + | a: bwtsw |
[bwa_aln] | [bwa_aln] | ||
− | n : | + | n: |
− | o : | + | o: |
− | e : | + | e: |
− | d : | + | d: |
− | i : | + | i: |
− | l : | + | l: |
− | k : | + | k: |
− | t : | + | t: 10 |
− | M : | + | M: |
− | O : | + | O: |
− | E : | + | E: |
− | R : | + | R: |
− | c : | + | c: |
− | N : | + | N: |
− | q : 18 | + | q: 18 |
− | I : | + | I: |
− | B : | + | B: |
− | b : | + | b: |
[bwa_sampe] | [bwa_sampe] | ||
− | a : | + | a: |
− | o : | + | o: |
− | P : TRUE | + | P: TRUE |
− | n : | + | n: |
− | N : | + | N: |
− | r : | + | r: |
######################### Picard ######################### | ######################### Picard ######################### | ||
# http://picard.sourceforge.net | # http://picard.sourceforge.net | ||
########################################################## | ########################################################## | ||
− | |||
− | |||
[MergeSamFiles] | [MergeSamFiles] | ||
− | VALIDATION_STRINGENCY : SILENT | + | VALIDATION_STRINGENCY: SILENT |
− | COMPRESSION_LEVEL : | + | COMPRESSION_LEVEL: |
− | MAX_RECORDS_IN_RAM : 30000000 | + | MAX_RECORDS_IN_RAM: 30000000 |
− | CREATE_INDEX : True | + | CREATE_INDEX: True |
− | SORT_ORDER : coordinate | + | SORT_ORDER: coordinate |
− | ASSUME_SORTED : True | + | ASSUME_SORTED: True |
− | MERGE_SEQUENCE_DICTIONARIES : | + | MERGE_SEQUENCE_DICTIONARIES: |
− | USE_THREADING : True | + | USE_THREADING: True |
− | COMMENT : | + | COMMENT: |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
[BuildBamIndex] | [BuildBamIndex] | ||
− | VALIDATION_STRINGENCY : SILENT | + | VALIDATION_STRINGENCY: SILENT |
− | COMPRESSION_LEVEL : | + | COMPRESSION_LEVEL: |
− | MAX_RECORDS_IN_RAM : | + | MAX_RECORDS_IN_RAM: |
− | CREATE_INDEX : | + | CREATE_INDEX: |
[CollectMultipleMetrics] | [CollectMultipleMetrics] | ||
− | ASSUME_SORTED : | + | ASSUME_SORTED: |
− | VALIDATION_STRINGENCY : SILENT | + | VALIDATION_STRINGENCY: SILENT |
− | PROGRAM : QualityScoreDistribution | + | PROGRAM: QualityScoreDistribution |
[MarkDuplicates] | [MarkDuplicates] | ||
− | VALIDATION_STRINGENCY : SILENT | + | VALIDATION_STRINGENCY: SILENT |
− | COMPRESSION_LEVEL : | + | COMPRESSION_LEVEL: |
− | MAX_RECORDS_IN_RAM : | + | MAX_RECORDS_IN_RAM: |
− | CREATE_INDEX : True | + | CREATE_INDEX: True |
− | PROGRAM_RECORD_ID : | + | PROGRAM_RECORD_ID: |
− | PROGRAM_GROUP_VERSION : | + | PROGRAM_GROUP_VERSION: |
− | PROGRAM_GROUP_COMMAND_LINE : | + | PROGRAM_GROUP_COMMAND_LINE: |
− | PROGRAM_GROUP_NAME : | + | PROGRAM_GROUP_NAME: |
− | COMMENT : | + | COMMENT: |
− | REMOVE_DUPLICATES : | + | REMOVE_DUPLICATES: |
− | ASSUME_SORTED : True | + | ASSUME_SORTED: True |
− | MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP : | + | MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP: |
− | MAX_FILE_HANDLES_FOR_READ_ENDS_MAP : | + | MAX_FILE_HANDLES_FOR_READ_ENDS_MAP: |
− | SORTING_COLLECTION_SIZE_RATIO : | + | SORTING_COLLECTION_SIZE_RATIO: |
− | READ_NAME_REGEX : | + | READ_NAME_REGEX: |
− | OPTICAL_DUPLICATE_PIXEL_DISTANCE : | + | OPTICAL_DUPLICATE_PIXEL_DISTANCE: |
− | |||
######################### GATK ########################### | ######################### GATK ########################### | ||
Line 223: | Line 215: | ||
[RealignerTargetCreator] | [RealignerTargetCreator] | ||
# inherited arguments | # inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | num_threads : | + | num_threads: 80 |
− | num_cpu_threads_per_data_thread : | + | num_cpu_threads_per_data_thread: |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
# specific arguments | # specific arguments | ||
− | maxIntervalSize : | + | maxIntervalSize: |
− | minReadsAtLocus : | + | minReadsAtLocus: |
− | mismatchFraction : | + | mismatchFraction: |
− | windowSize : | + | windowSize: |
[IndelRealigner] | [IndelRealigner] | ||
# inherited arguments | # inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | num_threads : | + | num_threads: |
− | num_cpu_threads_per_data_thread : | + | num_cpu_threads_per_data_thread: |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
# specific arguments | # specific arguments | ||
− | consensusDeterminationModel : | + | consensusDeterminationModel: |
− | knownAllele : | + | knownAllele: |
− | LODThresholdForCleaning : | + | LODThresholdForCleaning: |
− | nWayOut : | + | nWayOut: |
− | entropyThreshold : | + | entropyThreshold: |
− | maxConsensuses : | + | maxConsensuses: |
− | maxIsizeForMovement : | + | maxIsizeForMovement: |
− | maxPositionalMoveAllowed : | + | maxPositionalMoveAllowed: |
− | maxReadsForConsensuses : | + | maxReadsForConsensuses: |
− | maxReadsForRealignment : | + | maxReadsForRealignment: |
− | maxReadsInMemory : | + | maxReadsInMemory: |
− | noOriginalAlignmentTags : | + | noOriginalAlignmentTags: |
[BaseRecalibrator] | [BaseRecalibrator] | ||
# inherited arguments | # inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | num_threads : | + | num_threads: |
− | num_cpu_threads_per_data_thread : | + | num_cpu_threads_per_data_thread: 20 |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
# specific arguments | # specific arguments | ||
− | binary_tag_name : | + | binary_tag_name: |
− | covariate : | + | covariate: |
− | deletions_default_quality : | + | deletions_default_quality: |
− | indels_context_size : | + | indels_context_size: |
− | insertions_default_quality : | + | insertions_default_quality: |
− | low_quality_tail : | + | low_quality_tail: |
− | lowMemoryMode : | + | lowMemoryMode: |
− | maximum_cycle_value : | + | maximum_cycle_value: |
− | mismatches_context_size : | + | mismatches_context_size: |
− | mismatches_default_quality : | + | mismatches_default_quality: |
− | no_standard_covs : | + | no_standard_covs: |
− | quantizing_levels : | + | quantizing_levels: |
− | solid_nocall_strategy : | + | solid_nocall_strategy: |
− | solid_recal_mode : | + | solid_recal_mode: |
− | sort_by_all_columns : | + | sort_by_all_columns: |
− | |||
[PrintReads] | [PrintReads] | ||
# inherited arguments | # inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | num_cpu_threads_per_data_thread : | + | num_cpu_threads_per_data_thread: 20 |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
# specific arguments | # specific arguments | ||
− | downsample_coverage : | + | downsample_coverage: |
− | number : | + | number: |
− | platform : | + | platform: |
− | readGroup : | + | readGroup: |
− | sample_file : | + | sample_file: |
− | sample_name : | + | sample_name: |
− | simplify : | + | simplify: |
− | |||
[ReduceReads] | [ReduceReads] | ||
# inherited arguments | # inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
# specific arguments | # specific arguments | ||
− | cancer_mode : | + | cancer_mode: |
− | context_size : | + | context_size: |
− | dont_compress_read_names : | + | dont_compress_read_names: |
− | dont_hardclip_low_qual_tails : | + | dont_hardclip_low_qual_tails: |
− | dont_simplify_reads : | + | dont_simplify_reads: |
− | dont_use_softclipped_bases : | + | dont_use_softclipped_bases: |
− | downsample_coverage : | + | downsample_coverage: |
− | hard_clip_to_interval : | + | hard_clip_to_interval: |
− | known : | + | known: |
− | mindel : | + | mindel: |
− | minimum_mapping_quality : | + | minimum_mapping_quality: |
− | minimum_tail_qualities : | + | minimum_tail_qualities: |
− | minqual : | + | minqual: |
− | noclip_ad : | + | noclip_ad: |
− | out : | + | out: |
− | min_pvalue : | + | min_pvalue: |
− | minvar : | + | minvar: |
[UnifiedGenotyper] | [UnifiedGenotyper] | ||
# inherited arguments | # inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | num_threads : | + | num_threads: 8 |
− | num_cpu_threads_per_data_thread : | + | num_cpu_threads_per_data_thread: 10 |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
# specific arguments | # specific arguments | ||
− | alleles : | + | alleles: |
− | comp : | + | comp: |
− | dbsnp : | + | dbsnp: |
− | annotation : | + | annotation: |
− | contamination_fraction_per_sample_file : | + | contamination_fraction_per_sample_file: |
− | min_indel_fraction_per_sample | + | min_indel_fraction_per_sample: |
− | excludeAnnotation : | + | excludeAnnotation: |
− | genotype_likelihoods_model : BOTH | + | genotype_likelihoods_model: BOTH |
− | genotyping_mode : | + | genotyping_mode: |
− | group : | + | group: |
− | heterozygosity : | + | heterozygosity: |
− | indel_heterozygosity : | + | indel_heterozygosity: |
− | max_deletion_fraction : | + | max_deletion_fraction: |
− | min_base_quality_score : | + | min_base_quality_score: |
− | min_indel_count_for_genotyping : | + | min_indel_count_for_genotyping: |
− | pair_hmm_implementation : | + | pair_hmm_implementation: |
− | pcr_error_rate : | + | pcr_error_rate: |
− | sample_ploidy : | + | sample_ploidy: |
− | standard_min_confidence_threshold_for_calling | + | standard_min_confidence_threshold_for_calling: 30.0 |
− | standard_min_confidence_threshold_for_emitting : 30.0 | + | standard_min_confidence_threshold_for_emitting: 30.0 |
− | output_mode : EMIT_VARIANTS_ONLY | + | output_mode: EMIT_VARIANTS_ONLY |
− | annotateNDA : | + | annotateNDA: |
− | computeSLOD : | + | computeSLOD: |
− | indelGapContinuationPenalty : | + | indelGapContinuationPenalty: |
− | indelGapOpenPenalty : | + | indelGapOpenPenalty: |
− | input_prior : | + | input_prior: |
− | max_alternate_alleles : | + | max_alternate_alleles: |
− | onlyEmitSamples : | + | onlyEmitSamples: |
− | allSitePLs : | + | allSitePLs: |
[VariantRecalibrator_SNP] | [VariantRecalibrator_SNP] | ||
## inherited arguments | ## inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | num_threads : | + | num_threads: 40 |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
## specific arguments | ## specific arguments | ||
## required | ## required | ||
− | resource : hapmap,known=false,training=true,truth=true,prior=15.0 | + | resource: hapmap,known=false,training=true,truth=true,prior=15.0 |
− | resource : omni,known=false,training=true,truth=false,prior=12.0 | + | resource: omni,known=false,training=true,truth=false,prior=12.0 |
− | resource : 1000G,known=false,training=true,truth=false,prior=10.0 | + | resource: 1000G,known=false,training=true,truth=false,prior=10.0 |
− | use_annotation : QD | + | use_annotation: QD |
− | use_annotation : HaplotypeScore | + | use_annotation: HaplotypeScore |
− | use_annotation : MQRankSum | + | use_annotation: MQRankSum |
− | use_annotation : ReadPosRankSum | + | use_annotation: ReadPosRankSum |
− | use_annotation : FS | + | use_annotation: FS |
− | use_annotation : MQ | + | use_annotation: MQ |
#use_annotation : InbreedingCoeff | #use_annotation : InbreedingCoeff | ||
## optional | ## optional | ||
− | dirichlet : | + | dirichlet: |
− | ignore_filter : | + | ignore_filter: |
− | maxGaussians : | + | maxGaussians: |
− | maxIterations : | + | maxIterations: |
− | numBadVariants : 1000 | + | numBadVariants: 1000 |
− | numKMeans : | + | numKMeans: |
− | priorCounts : | + | priorCounts: |
− | qualThreshold : | + | qualThreshold: |
− | shrinkage : | + | shrinkage: |
− | stdThreshold : | + | stdThreshold: |
− | target_titv : | + | target_titv: |
− | ts_filter_level : | + | ts_filter_level: |
− | TStranche : | + | TStranche: |
− | maxNegativeGaussians : | + | maxNegativeGaussians: |
− | trustAllPolymorphic : | + | trustAllPolymorphic: |
− | |||
[VariantRecalibrator_INDEL] | [VariantRecalibrator_INDEL] | ||
## inherited arguments | ## inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | num_threads : | + | num_threads: 40 |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
## specific arguments | ## specific arguments | ||
## required | ## required | ||
− | resource : mills,known=false,training=true,truth=true,prior=12.0 | + | resource: mills,known=false,training=true,truth=true,prior=12.0 |
− | resource : dbsnp,known=true,training=false,truth=false,prior=2.0 | + | resource: dbsnp,known=true,training=false,truth=false,prior=2.0 |
− | use_annotation : MQRankSum | + | use_annotation: MQRankSum |
− | use_annotation : ReadPosRankSum | + | use_annotation: ReadPosRankSum |
− | use_annotation : FS | + | use_annotation: FS |
− | use_annotation : DP | + | use_annotation: DP |
## optional | ## optional | ||
− | dirichlet : | + | dirichlet: |
− | ignore_filter : | + | ignore_filter: |
− | maxGaussians : 4 | + | maxGaussians: 4 |
− | maxIterations : | + | maxIterations: |
− | numBadVariants : 1000 | + | numBadVariants: 1000 |
− | numKMeans : | + | numKMeans: |
− | priorCounts : | + | priorCounts: |
− | qualThreshold : | + | qualThreshold: |
− | shrinkage : | + | shrinkage: |
− | stdThreshold : | + | stdThreshold: |
− | target_titv : | + | target_titv: |
− | ts_filter_level : | + | ts_filter_level: |
− | TStranche : | + | TStranche: |
− | maxNegativeGaussians : | + | maxNegativeGaussians: |
− | trustAllPolymorphic : | + | trustAllPolymorphic: |
[ApplyRecalibration_SNP] | [ApplyRecalibration_SNP] | ||
## inherited arguments | ## inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | num_threads : | + | num_threads: 40 |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
## specific arguments | ## specific arguments | ||
− | ts_filter_level : 99.0 | + | ts_filter_level: 99.0 |
− | |||
[ApplyRecalibration_INDEL] | [ApplyRecalibration_INDEL] | ||
## inherited arguments | ## inherited arguments | ||
− | analysis_type : | + | analysis_type: |
− | baq : | + | baq: |
− | baqGapOpenPenalty : | + | baqGapOpenPenalty: |
− | BQSR : | + | BQSR: |
− | defaultBaseQualities : | + | defaultBaseQualities: |
− | disable_indel_quals : | + | disable_indel_quals: |
− | downsample_to_coverage : | + | downsample_to_coverage: |
− | downsample_to_fraction : | + | downsample_to_fraction: |
− | downsampling_type : | + | downsampling_type: |
− | emit_original_quals : | + | emit_original_quals: |
− | excludeIntervals : | + | excludeIntervals: |
− | gatk_key : | + | gatk_key: |
− | globalQScorePrior : | + | globalQScorePrior: |
− | interval_merging : | + | interval_merging: |
− | interval_padding : | + | interval_padding: |
− | interval_set_rule : | + | interval_set_rule: |
− | intervals : | + | intervals: |
− | keep_program_records : | + | keep_program_records: |
− | log_to_file : | + | log_to_file: |
− | logging_level : | + | logging_level: |
− | maxRuntime : | + | maxRuntime: |
− | maxRuntimeUnits : | + | maxRuntimeUnits: |
− | monitorThreadEfficiency : | + | monitorThreadEfficiency: |
− | nonDeterministicRandomSeed : | + | nonDeterministicRandomSeed: |
− | num_bam_file_handles : | + | num_bam_file_handles: |
− | num_threads : | + | num_threads: 40 |
− | pedigree : | + | pedigree: |
− | pedigreeString : | + | pedigreeString: |
− | pedigreeValidationType : | + | pedigreeValidationType: |
− | performanceLog : | + | performanceLog: |
− | phone_home : | + | phone_home: |
− | preserve_qscores_less_than : | + | preserve_qscores_less_than: |
− | read_buffer_size : | + | read_buffer_size: |
− | read_filter : | + | read_filter: |
− | read_group_black_list : | + | read_group_black_list: |
− | reference_sequence : | + | reference_sequence: |
− | remove_program_records : | + | remove_program_records: |
− | tag : | + | tag: |
− | unsafe : | + | unsafe: |
− | useOriginalQualities : | + | useOriginalQualities: |
− | validation_strictness : | + | validation_strictness: |
− | allowBqsrOnReducedBams : | + | allowBqsrOnReducedBams: |
## specific arguments | ## specific arguments | ||
− | ts_filter_level : 99.0 | + | ts_filter_level: 99.0 |
+ | |||
</pre> | </pre> |
Latest revision as of 16:54, 3 October 2013
############################################################# ############################################################# ################## cApTUrE config file ##################### ############################################################# ############################################################# ## Pipeline uses Illumina file naming conventions. This naming convention is described here: ## http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_FASTQFiles.htm ## The sample name and lane information of the fastq file are the most important parts for the pipeline to work correctly. ## Boolean options must be specified as TRUE (false values as blanks). [required] # ugp_id is a unique identifier for each project in the format UGP_0001 ugp_id: UGP_0001 # ugp_verson describes the version of the pipeline used ugp_version: 0.0.2 # location of md5 file to check data integrity md5: /home/srynearson/cApTUrE/Fastq/<FILE> # The path to the reference genome fasta file (include file) fasta: /home/srynearson/cAPTUrE/references/human_g1k_v37.fasta # The path to the project fastq files. # include trailing slash! fastq_dir: /data/srynearson/Fastq/ # The name of the command line and pipeline info log file command_log: cmd.log # The number of CPUs available for Perl to parallel process # Matching to number of fastq file works best cpu: 8 # The Xmx (memory usage) for Picard tools # max shoud be set to 125 picard_java_Xmx: 50 # The Xmx (memory usage) for GATK RealignerTargetCreator gatk_tc_Xmx: 125 # The Xmx (memory usage) for GATK IndelRealigner gatk_ir_Xmx: 125 # The Xmx (memory usage) for GATK BaseRecalibrator gatk_br_Xmx: 125 # The Xmx (memory usage) for PrintReads gatk_pr_Xmx: 125 # The Xmx (memory usage) for ReduceReads gatk_rr_Xmx: 125 # The Xmx (memory usage) for UnifiedGenotyper gatk_ug_Xmx: 125 # The path to temp dir used by java java_tmp: /tmp/ # Path to VCF files for RealignerTargetCreator knowns known_indel: /home/srynearson/cAPTUrE/background_files/known_indels known_dbSNP: /home/srynearson/cAPTUrE/background_files/known_dbSNP # Path to background bams used running UnifiedGenotyper # not required to run but will improve variant calls unified_bg_bams: /data/srynearson/reducedreads/ # Resource files (including path) for VariantRecalibrator_SNP # Order must match VariantRecalibrator_SNP option below! vqsr_snp_vcf: /data/srynearson/resources/hapmap_3.3.b37.vcf vqsr_snp_vcf: /data/srynearson/resources/1000G_omni2.5.b37.vcf vqsr_snp_vcf: /data/srynearson/resources/1000G_phase1.snps.high_confidence.b37.vcf # Resource files (including path) for VariantRecalibrator_INDEL # Order must match VariantRecalibrator_INDEL option below! vsqr_indel_vcf: /data/srynearson/resources/Mills_and_1000G_gold_standard.indels.b37.vcf vsqr_indel_vcf: /data/srynearson/resources/dbsnp_137.b37.vcf # path to needed software(required). [software] bwa: /usr/local/bwa/ fastqc: /usr/local/FastQC/ picard: /usr/local/picard-tools/ samtools: /usr/local/samtools/ gatk: /usr/local/GenomeAnalysisTK-2.7-2/GenomeAnalysisTK.jar # Pipeline Run Order. [order] ## requires at least two commands to be used #command_order : indexer command_order: fastqc command_order: bwa_aln command_order: bwa_sampe command_order: idxstats command_order: flagstat command_order: MergeSamFiles command_order: MarkDuplicates command_order: RealignerTargetCreator command_order: IndelRealigner command_order: BaseRecalibrator command_order: PrintReads command_order: CollectMultipleMetrics command_order: ReduceReads command_order: UnifiedGenotyper command_order: VariantRecalibrator command_order: ApplyRecalibration # VariantRecalibrator will run both SNP and INDEL version # can be ran independently if desired. #command_order : VariantRecalibrator_SNP #command_order : VariantRecalibrator_INDEL #command_order : ApplyRecalibration_SNP #command_order : ApplyRecalibration_INDEL ######################### FASTQC ############################ # http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ############################################################# [fastqc] outdir: extract: threads: 10 kmers: quiet: ######################### BWA ############################### # http://bio-bwa.sourceforge.net/bwa.shtml ############################################################# [bwa_index] p: a: bwtsw [bwa_aln] n: o: e: d: i: l: k: t: 10 M: O: E: R: c: N: q: 18 I: B: b: [bwa_sampe] a: o: P: TRUE n: N: r: ######################### Picard ######################### # http://picard.sourceforge.net ########################################################## [MergeSamFiles] VALIDATION_STRINGENCY: SILENT COMPRESSION_LEVEL: MAX_RECORDS_IN_RAM: 30000000 CREATE_INDEX: True SORT_ORDER: coordinate ASSUME_SORTED: True MERGE_SEQUENCE_DICTIONARIES: USE_THREADING: True COMMENT: [BuildBamIndex] VALIDATION_STRINGENCY: SILENT COMPRESSION_LEVEL: MAX_RECORDS_IN_RAM: CREATE_INDEX: [CollectMultipleMetrics] ASSUME_SORTED: VALIDATION_STRINGENCY: SILENT PROGRAM: QualityScoreDistribution [MarkDuplicates] VALIDATION_STRINGENCY: SILENT COMPRESSION_LEVEL: MAX_RECORDS_IN_RAM: CREATE_INDEX: True PROGRAM_RECORD_ID: PROGRAM_GROUP_VERSION: PROGRAM_GROUP_COMMAND_LINE: PROGRAM_GROUP_NAME: COMMENT: REMOVE_DUPLICATES: ASSUME_SORTED: True MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP: MAX_FILE_HANDLES_FOR_READ_ENDS_MAP: SORTING_COLLECTION_SIZE_RATIO: READ_NAME_REGEX: OPTICAL_DUPLICATE_PIXEL_DISTANCE: ######################### GATK ########################### # http://www.broadinstitute.org/gatk/ ############################################################ [RealignerTargetCreator] # inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: num_threads: 80 num_cpu_threads_per_data_thread: pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: # specific arguments maxIntervalSize: minReadsAtLocus: mismatchFraction: windowSize: [IndelRealigner] # inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: num_threads: num_cpu_threads_per_data_thread: pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: # specific arguments consensusDeterminationModel: knownAllele: LODThresholdForCleaning: nWayOut: entropyThreshold: maxConsensuses: maxIsizeForMovement: maxPositionalMoveAllowed: maxReadsForConsensuses: maxReadsForRealignment: maxReadsInMemory: noOriginalAlignmentTags: [BaseRecalibrator] # inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: num_threads: num_cpu_threads_per_data_thread: 20 pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: # specific arguments binary_tag_name: covariate: deletions_default_quality: indels_context_size: insertions_default_quality: low_quality_tail: lowMemoryMode: maximum_cycle_value: mismatches_context_size: mismatches_default_quality: no_standard_covs: quantizing_levels: solid_nocall_strategy: solid_recal_mode: sort_by_all_columns: [PrintReads] # inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: num_cpu_threads_per_data_thread: 20 pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: # specific arguments downsample_coverage: number: platform: readGroup: sample_file: sample_name: simplify: [ReduceReads] # inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: # specific arguments cancer_mode: context_size: dont_compress_read_names: dont_hardclip_low_qual_tails: dont_simplify_reads: dont_use_softclipped_bases: downsample_coverage: hard_clip_to_interval: known: mindel: minimum_mapping_quality: minimum_tail_qualities: minqual: noclip_ad: out: min_pvalue: minvar: [UnifiedGenotyper] # inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: num_threads: 8 num_cpu_threads_per_data_thread: 10 pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: # specific arguments alleles: comp: dbsnp: annotation: contamination_fraction_per_sample_file: min_indel_fraction_per_sample: excludeAnnotation: genotype_likelihoods_model: BOTH genotyping_mode: group: heterozygosity: indel_heterozygosity: max_deletion_fraction: min_base_quality_score: min_indel_count_for_genotyping: pair_hmm_implementation: pcr_error_rate: sample_ploidy: standard_min_confidence_threshold_for_calling: 30.0 standard_min_confidence_threshold_for_emitting: 30.0 output_mode: EMIT_VARIANTS_ONLY annotateNDA: computeSLOD: indelGapContinuationPenalty: indelGapOpenPenalty: input_prior: max_alternate_alleles: onlyEmitSamples: allSitePLs: [VariantRecalibrator_SNP] ## inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: num_threads: 40 pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: ## specific arguments ## required resource: hapmap,known=false,training=true,truth=true,prior=15.0 resource: omni,known=false,training=true,truth=false,prior=12.0 resource: 1000G,known=false,training=true,truth=false,prior=10.0 use_annotation: QD use_annotation: HaplotypeScore use_annotation: MQRankSum use_annotation: ReadPosRankSum use_annotation: FS use_annotation: MQ #use_annotation : InbreedingCoeff ## optional dirichlet: ignore_filter: maxGaussians: maxIterations: numBadVariants: 1000 numKMeans: priorCounts: qualThreshold: shrinkage: stdThreshold: target_titv: ts_filter_level: TStranche: maxNegativeGaussians: trustAllPolymorphic: [VariantRecalibrator_INDEL] ## inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: num_threads: 40 pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: ## specific arguments ## required resource: mills,known=false,training=true,truth=true,prior=12.0 resource: dbsnp,known=true,training=false,truth=false,prior=2.0 use_annotation: MQRankSum use_annotation: ReadPosRankSum use_annotation: FS use_annotation: DP ## optional dirichlet: ignore_filter: maxGaussians: 4 maxIterations: numBadVariants: 1000 numKMeans: priorCounts: qualThreshold: shrinkage: stdThreshold: target_titv: ts_filter_level: TStranche: maxNegativeGaussians: trustAllPolymorphic: [ApplyRecalibration_SNP] ## inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: num_threads: 40 pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: ## specific arguments ts_filter_level: 99.0 [ApplyRecalibration_INDEL] ## inherited arguments analysis_type: baq: baqGapOpenPenalty: BQSR: defaultBaseQualities: disable_indel_quals: downsample_to_coverage: downsample_to_fraction: downsampling_type: emit_original_quals: excludeIntervals: gatk_key: globalQScorePrior: interval_merging: interval_padding: interval_set_rule: intervals: keep_program_records: log_to_file: logging_level: maxRuntime: maxRuntimeUnits: monitorThreadEfficiency: nonDeterministicRandomSeed: num_bam_file_handles: num_threads: 40 pedigree: pedigreeString: pedigreeValidationType: performanceLog: phone_home: preserve_qscores_less_than: read_buffer_size: read_filter: read_group_black_list: reference_sequence: remove_program_records: tag: unsafe: useOriginalQualities: validation_strictness: allowBqsrOnReducedBams: ## specific arguments ts_filter_level: 99.0