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>
 +
 
#############################################################
 
#############################################################
 
#############################################################
 
#############################################################
Line 10: Line 11:
 
## 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_0003
+
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         : /home/srynearson/cApTUrE/Fastq/<FILE>
+
md5: /home/srynearson/cApTUrE/Fastq/<FILE>
  
# The path to the reference genome fasta file (including file)
+
# The path to the reference genome fasta file (include file)
fasta       : /home/srynearson/cAPTUrE/references/human_g1k_v37.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   : /data/srynearson/Fastq/
+
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   : cmd.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         : 8
+
# Matching to number of fastq file works best
 +
cpu: 8
  
# The Xmx (memory usage) for picard
+
# The Xmx (memory usage) for Picard tools
picard_java_Xmx : 130
+
# 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 : 20 
+
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 : 40
+
gatk_ug_Xmx: 125
  
# The path to temp files used by java
+
# The path to temp dir used by java
java_tmp   : /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     : /usr/local/bwa/  
+
bwa: /usr/local/bwa/
fastqc   : /usr/local/FastQC/
+
fastqc: /usr/local/FastQC/
picard   : /usr/local/picard-tools/
+
picard: /usr/local/picard-tools/
samtools : /usr/local/samtools/
+
samtools: /usr/local/samtools/
gatk     : /usr/local/GenomeAnalysisTK-2.7-2/GenomeAnalysisTK.jar
+
gatk: /usr/local/GenomeAnalysisTK-2.7-2/GenomeAnalysisTK.jar
 
 
# Pipeline Order
 
  
 +
# 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: 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
# But they can be ran independent if desired
+
# 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 : 9
+
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 : 9
+
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
 
##########################################################
 
##########################################################
 
[picard_java]
 
  
 
[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:  
 
 
[SortSam]
 
VALIDATION_STRINGENCY : SILENT
 
COMPRESSION_LEVEL :
 
MAX_RECORDS_IN_RAM :
 
CREATE_INDEX : True
 
SORT_ORDER : coordinate
 
  
 
[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 : 50
+
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 : 9
+
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 : 9
+
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 : 25
+
num_threads: 8
num_cpu_threads_per_data_thread : 3
+
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 : 30.0
+
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 : 37
+
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 : 37
+
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 : 37
+
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 : 37
+
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