NGS Data QC
Implementation of the ngs_data_qc
step
Default Configuration
The default configuration is as follows.
# Default configuration ngs_mapping
step_config:
ngs_data_qc:
path_link_in: "" # OPTIONAL Override data set configuration search paths for FASTQ files
tools: [fastqc, picard] # REQUIRED - available: 'fastqc' & 'picard' (for QC on bam files)
picard:
path_ngs_mapping: ../ngs_mapping # REQUIRED
path_to_baits: "" # Required when CollectHsMetrics is among the programs
path_to_targets: "" # When missing, same as baits
bait_name: "" # Exon enrichment kit name (optional)
programs: [] # Available metrics:
# * Generic metrics [* grouped into CollectMultipleMetrics]
# - CollectAlignmentSummaryMetrics *
# - CollectBaseDistributionByCycle *
# - CollectGcBiasMetrics *
# - CollectInsertSizeMetrics *
# - CollectJumpingLibraryMetrics
# - CollectOxoGMetrics
# - CollectQualityYieldMetrics *
# - CollectSequencingArtifactMetrics *
# - EstimateLibraryComplexity
# - MeanQualityByCycle *
# - QualityScoreDistribution *
# * WGS-specific metrics
# - CollectRawWgsMetrics
# - CollectWgsMetrics
# - CollectWgsMetricsWithNonZeroCoverage
# * Other assay-specific metrics
# - CollectHsMetrics Whole Exome Sequencing
# - CollectTargetedPcrMetrics Panel sequencing
# - CollectRnaSeqMetrics mRNA sequencing, not implemented yet
# - CollectRbsMetrics bi-sulfite sequencing, not implemented yet