Trio analysis

• Trio Analysis: trio analysis for the case of a proband child and unaffected parents has been implemented.
• Modularisation: the pipeline has been restructured to be modular so that other types of analyses can be added to the system.
• Gap file annotation: more complete and extensible gap annotation functionality has been implemented.
• Tool Updates: all 3rd party tools have been updated to the latest versions.
• Migration to VEP and removal of Annovar dependency: Annovar is no longer part of the analysis. All annotation is performed by VEP, along with VEP plugins.
• LOVD+ Compatibility: The final output is a tab separated file that complies with LOVD+ requirements.
  Support for both BED file and gene list inputs: Analysis profiles can be specified with either regions (BED) or gene lists.
• Improved test framework: The testability and robustness of the code has been improved.
• Additional configuration options:
  • ANNOTATE_CUSTOM_REGIONS="": bed file to add additional annotation to the final output.
  • FILTERED_ON_EXONS="skip": what kind of final bam file to generate (skip, design, or exons)
  • GAP_ANNOTATOR_CUSTOM_BEDS="": space separated list of additonal bed files to consult when generating the gap annotation file.
  • GATK_VARIANT_ONLY=false: do not do genotyping, directly call the variants.
  • POST_ANALYSIS_READ_ONLY=true: mark the batch read only on completion.
  • POST_ANALYSIS_MOVE=true: move the batch directory on completion.
  • HARD_FILTER_AD=2: minimum allele depth
  • HARD_FILTER_AF=0.15: minimum allele frequency
  • HARD_FILTER_DP=5: minimum depth
  • HARD_FILTER_QUAL=5: minimum quality
  • QC_THRESHOLD=20: what depth is required to contribute to satisfactory coverage
  • QC_GOOD=95: what percentage of QC_THRESHOLD must be achieved across the gene to get a good rating
  • QC_PASS=80: what percentage of QC_THRESHOLD must be achieved across the gene to get a pass rating
  • QC_FAIL=0: what percentage of QC_THRESHOLD must be achieved across the gene to get a fail rating