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 It is preserved here for archival and historical reference only.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.
Compare PHG variants to existing variants¶
Quick Start¶
- Change Truth_set.vcf,
param3, andparam4in your config file to match file paths on your computer. - Run phg VCF_compare [config.txt]
Process Details¶
This process does not exist formally at the moment. But one can imagine basically specifying a trustworth VCF with high confidence SNPs and comparing to those variants imputed from PHG and computing accuracy.