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s-andrews / BamQC

Mapped QC analysis program
GNU General Public License v3.0
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Module thresholds (WARN / ERROR) #5

Open pdp10 opened 8 years ago

pdp10 commented 8 years ago

we need to define module-specific thresholds triggering potential warnings or errors.

pdp10 commented 6 years ago

First draft of thresholds. 

# BamQC configuration file

####################
# MODULE SELECTION #
####################

# For each of the modules you can choose to not run that
# module at all by setting the value below to 1 for the
# modules you want to remove.
ChromosomeReadDensity                   ignore  0
FeatureCoverage                     ignore  0
GenomeCoverage                      ignore  0
IndelFrequencies                    ignore  0
InsertLengthDistribution                ignore  0
MappingQualityDistribution              ignore  0
# deprecated
SequenceQualityDistribution             ignore  1
SNPFrequencies                      ignore  0
SNPFrequenciesByType                    ignore  0
SoftClipDistribution                    ignore  0
# The following option turns off InsertFrequencies, 
# SNPFrequencies, SNPFrequenciesByType, 
# and some statistics in BasicStatistics
VariantCallDetection                    ignore  0

##############################
# MODULE-SPECIFIC THRESHOLDS #
##############################

# BasicStatistics module
BasicStatistics_unmapped_percent_threshold  warn    50  
BasicStatistics_unmapped_percent_threshold  error   90

# ChromosomeReadDensity Module
ChromosomeReadDensity_readNumber_threshold  warn    25
ChromosomeReadDensity_readNumber_threshold  error   10

# GenomeCoverage module
GenomeCoverage_plot_type_chromosomes_threshold      ignore  50
GenomeCoverage_plot_bins_all_chromosomes        ignore  5000        
GenomeCoverage_plot_bins_per_chromosome         ignore  500
GenomeCoverage_uncovered_genome_percent_threshold   error   10
GenomeCoverage_uncovered_genome_percent_threshold   warn    5

# Indel/SNP modules     
VariantCallPosition_indel_seqpercent_xaxis_threshold    ignore      5
VariantCallPosition_indel_max_freq_threshold        warn        5   
VariantCallPosition_indel_max_freq_threshold        error       25
VariantCallPosition_snp_seqpercent_xaxis_threshold      ignore      5       
VariantCallPosition_snp_max_freq_threshold          warn        5   
VariantCallPosition_snp_max_freq_threshold          error       25
VariantCallPosition_snp_max_freq_by_type_threshold  warn        0.5 
VariantCallPosition_snp_max_freq_by_type_threshold  error       2.5

# Insert Length Distribution module
InsertLengthDistribution_max_insert_size        ignore      10000.0
InsertLengthDistribution_bin_size               ignore      1.0
InsertLengthDistribution_percentage_deviation       error       75.0
InsertLengthDistribution_percentage_deviation       warn        50.0

# MappingQualityDistribution module
MappingQualityDistribution_fraction         error  0.50
MappingQualityDistribution_fraction         warn   0.75

# SoftClipDistribution module 
SoftClipDistribution_clip_number_threshold  error   100
SoftClipDistribution_clip_number_threshold  warn    25

# Annotation Module
AnnotationSet_annotation_cache_capacity     ignore   50000

#################################################
# MODULES WITH CURRENTLY NO EXPLICIT THRESHOLDS #
#################################################
# FeatureCoverage module
pdp10 commented 6 years ago

Merged to develop branch. See PR #32 .