Find haplotype clusters 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 It is preserved here for archival and historical reference only.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 FindHaplotypeClustersPlugin processes a multi-haplotype VCF file from one region, and identifies haplotype clusters to be collapsed into a consensus haplotype. For every alignment in a genotype table, taxa are filtered by coverage to create clusters. The clusters are determined based on number of alignments without indels, a specified minimum number of polymorphic sites to calculate identity and a maximum distance from each taxon. The resulting clusters are filtered again based on a minimum number of taxa in each group. Those clusters passing the filtering criteria have their sequence pulled and written to a fasta file for loading to the PHG DB haplotypes table.

The parameters for this plugin are:

  • -ref input Reference fasta for pulling reference sequence where gvcf indicates REFRANGE. (Default=null) (REQUIRED)
  • -haplotypeMethod Name of haplotype method to sue when retrieving haplotypes form the graph. Must be a method currently stored in the PHG db methods table. (Default=null) (REQUIRED)
  • -dbConfigFile File holding configuration information for connecting to the PHG DB. (Default=null) (REQUIRED)
  • -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)