Paths to VCF 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 It is preserved here for archival and historical reference only.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 PathsToVCFPlugin is used to create VCF files from haplotype paths. The user may specific specific reference ranges to be included in the exported file. This plugin would likely be chained with the HaplotypeGraphBuilderPlugin and the ImportHaplotypePathFilePlugin. It takes input from both and uses this to create the requested VCF files.

The parameters to this plugin are:

  • -outputFile The file name for storing the VCF data. (Default=null) (REQUIRED)
  • -RefRangeFileVCF Reference Range file used to further subset the paths for only specified regions of the genome. It not provided, all references ranges are used. (Default=null) (OPTIONAL)