Merge GVCF 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 It is preserved here for archival and historical reference only.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 plugin MergeGVCFPlugin pulls the variant context records stored in the database for all of the taxon at each reference range stored against a specified method id. The calls and depth information are merged into a single VariantContext record to later be read into the FindHaplotypeClustersPlugin.

The plugin requires a PHG Haplotype Graph as well as a GenomeSequence object. MergeGVCFPlugin is currently invoked from the RunHapCollapsePlugin, which passes these objects via the DataSet parameter.

The parameters to this plugin are:

• -outputDir
  The direcotry where the output VCF files will be stored. (Default=null) (OBSOLETE)
• -dbConfig < DB Config File> Config file containing properties host,user,password,DB and DBtype where DBtype is either sqlite or postgres.
• -hapMethod Name of the method used to call the haplotypes. This must match the method name as stored in the database methods table. It is needed to pull the correct sub-graph.