Run hap collapse plugin

Legacy Documentation - PHG Version 1

This section contains documentation for PHG version 1, which is no longer actively developed. It is preserved here for archival and historical reference only. If you are looking to use the Practical Haplotype Graph, please refer to the PHG v2 documentation, which reflects the current version of the software.

The RunHapCollapsePlugin method was written to consolidate calls to the collapse pipeline. Invocation of this plugin results in the following functionality performed:

Loop through each reference range in the graph:

  • Extract the HaplotypeNodes with the VariantContexts (we assume that the user has not pulled these yet for memory reasons)
  • Merge all the VariantContext records for each base pair (bp) of the reference range
  • Export a GenotypeTable containing each bp
  • Run HapCollapse Finding algorithm on this genotype table

For each VCF file exported, upload them to the DB as a consensus

The parameters to this plugin are:

  • -mergedOutputDir Directory to store the ouput VCFs from the merge process. (Default=null)(REQUIRED)
  • -ref Input reference fasta to be passed to FindHaplotypeClusters for extracting reference sequence.
  • -haplotypeMethod Haplotype calling method used to retrieve the correct haplotypes from the graph. (Default=null) (REQUIRED)
  • -dbConfigFile File holding the database configuration information.
  • -consensusVCFOutputDir Directory in which to store the output VCFs from the consensus process. (Default=null) (REQUIRED)
  • -consensusFastaOutputDir Directory in which to store the output fastas from the consensus process. (Default=null) (REQUIRED)
  • -refVersion Version name of the reference intervals. Must match a version name that is stored in the genome_interval_versions DB table. (Default=null) (REQUIRED)
  • -collapseMethod Name to be stored in the DB for this method used to collapse the haplotypes into consensus sequences. (Default=null) (REQUIRED)
  • collapseMethodDetails Details describing the collapse method. (Default=null) (REQUIRED)

This method calls FindHaplotypeClustersPlugin/MergeGVCFPlugin in parallel for each reference range to create the haplotype clusters. The resulting consensus sequences are loaded to the haplotypes table via a call to LoadConsensusAnchorSequencesPlugin.