View source for UGP Pipeline Config Template 0.0.2

<pre>

#############################################################
# REQUIRED OPTIONS
#############################################################

# 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

[argv]

# 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

# ugp_name is a human readable name for the analysis (alphanumeric charachters and underscores only - no spaces).
ugp_name    : Shawn_Genome

# The location of the reference genome fasta file
fasta       : /home/srynearson/UGP_Pipeline/data/reference/human_g1k_v37.fasta

# The path to the project fastq files
fastq_dir   : /home/srynearson/UGP_Pipeline/data/SGF65/

# The name of the error log file
error_log   : error.log

# The name of the command line log file 
cmd_log     : cmd.log 

# The number of CPUs available for analysis
cpu         : 10

# The Xmx (memory usage) argument given to Java
java_Xmx    : 8

# The path to temp files used by java
java_tmp    : /tmp/

# Path to VCF files for realignment
known_indel : /home/srynearson/UGP_Pipeline/data/known_indels/
known_dbSNP : /home/srynearson/UGP_Pipeline/data/known_dbSNP/

# Path to background for Unified variant calling
unified_background :

# Software paths
bwa      : /usr/local/bwa/
fastqc   : /usr/local/FastQC/
samtools : /usr/local/samtools/
picard   : /usr/local/picard-tools-1.90/
gatk     : /usr/local/GenomeAnalysisTK-2.6-5/GenomeAnalysisTK.jar

# Pipeline Order

######################### FASTQC ############################
# http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
#############################################################

[fastqc]
outdir  :  
extract : 
threads : 4
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 : 15
I : 
B :
b :

[bwa_sampe]
a :
o :
P : TRUE
n :
N : 
r :

######################### Picard #########################
# http://picard.sourceforge.net
##########################################################

[AddOrReplaceReadGroups]
VALIDATION_STRINGENCY : SILENT
COMPRESSION_LEVEL : 
MAX_RECORDS_IN_RAM : 2000000 
CREATE_INDEX : true
SORT_ORDER : coordinate 
RGPL : illumina 
RGPU : 1
RGSM : 
RGCN : 
RGDS : 
RGDT : 

[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 : 

[FixMateInformation]
VALIDATION_STRINGENCY : SILENT
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :
SORT_ORDER : coordinate

[SortSam]
VALIDATION_STRINGENCY : LENIENT
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :
SORT_ORDER : coordinate 

[BuildBamIndex]
VALIDATION_STRINGENCY :
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :

[MarkDuplicates]
VALIDATION_STRINGENCY : SILENT
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :
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 : 

[CollectAlignmentSummaryMetrics]
VALIDATION_STRINGENCY :
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :
X_INSERT_SIZE : 
ADAPTER_SEQUENCE : 
METRIC_ACCUMULATION_LEVEL : 
IS_BISULFITE_SEQUENCED : 
REFERENCE_SEQUENCE : 
ASSUME_SORTED : 
STOP_AFTER : 

[CollectGcBiasMetrics]
VALIDATION_STRINGENCY :
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :
REFERENCE_SEQUENCE : 
CHART_OUTPUT : 
SUMMARY_OUTPUT : 
WINDOW_SIZE : 
MINIMUM_GENOME_FRACTION : 
ASSUME_SORTED : 
IS_BISULFITE_SEQUENCED : 

[CollectInsertSizeMetrics]
VALIDATION_STRINGENCY :
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :
HISTOGRAM_FILE : 
DEVIATIONS : 
HISTOGRAM_WIDTH : 
MINIMUM_PCT : 
METRIC_ACCUMULATION_LEVEL : 
REFERENCE_SEQUENCE : 
ASSUME_SORTED : 
STOP_AFTER : 

[MeanQualityByCycle]
VALIDATION_STRINGENCY :
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :
CHART_OUTPUT : 
ALIGNED_READS_ONLY : 
PF_READS_ONLY : 
REFERENCE_SEQUENCE : 
ASSUME_SORTED : 
STOP_AFTER : 

[QualityScoreDistribution]
VALIDATION_STRINGENCY :
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :
CHART_OUTPUT : 
ALIGNED_READS_ONLY : 
PF_READS_ONLY : 
INCLUDE_NO_CALLS : 
REFERENCE_SEQUENCE : 
ASSUME_SORTED : 
STOP_AFTER : 

[BamIndexStats]
VALIDATION_STRINGENCY :
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :

[CalculateHsMetrics]
VALIDATION_STRINGENCY :
COMPRESSION_LEVEL :
MAX_RECORDS_IN_RAM :
CREATE_INDEX :
BAIT_INTERVALS : 
BAIT_SET_NAME : 
TARGET_INTERVALS : 
METRIC_ACCUMULATION_LEVEL : 
REFERENCE_SEQUENCE : 
PER_TARGET_COVERAGE : 

######################### GATK ###########################
# http://www.broadinstitute.org/gatk/
############################################################

[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 :
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 :
annotateNDA :
computeSLOD :
dbsnp :
excludeAnnotation :
genotype_likelihoods_model :
genotyping_mode :
group :
heterozygosity :
indel_heterozygosity :
max_deletion_fraction :
min_base_quality_score :
output_mode :
pair_hmm_implementation :
pcr_error_rate :
sample_ploidy :
allSitePLs :
indelGapContinuationPenalty :
indelGapOpenPenalty :
input_prior :
max_alternate_alleles :

[VariantRecalibrator]
# 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 :
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
recal_file :
resource :
tranches_file :
use_annotation :
dirichlet :
ignore_filter :
maxGaussians :
maxIterations :
minNumBadVariants :
mode :
numKMeans :
percentBadVariants :
priorCounts :
qualThreshold :
rscript_file :
shrinkage :
stdThreshold :
target_titv :
ts_filter_level :
TStranche :
trustAllPolymorphic :

[ApplyRecalibration]
# 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 :
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
tranches_file :
ignore_filter :
mode :
ts_filter_level :


[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 : 24
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 :
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 :
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 : 

[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 :
num_threads :
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 :

[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_threads :
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 :

[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 :
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 :
genotyping_mode :
group :
heterozygosity :
indel_heterozygosity :
max_deletion_fraction :
min_base_quality_score :
min_indel_count_for_genotyping :
output_mode :
pair_hmm_implementation :
pcr_error_rate :
sample_ploidy :
standard_min_confidence_threshold_for_calling  :
standard_min_confidence_threshold_for_emitting :
annotateNDA :
computeSLOD :
indelGapContinuationPenalty :
indelGapOpenPenalty :
input_prior :
max_alternate_alleles :
onlyEmitSamples :
allSitePLs :

</pre>