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 It is preserved here for archival and historical reference only.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.

ConfigFile Documentation

Most steps of the Practical Haplotype Graph require a Configuration File. For the most part, users can create one config file and add parameters when needed, reusing it along the way.

Sample Configuration File

Here is a sample configuration file. This file contains the required parameters and some additional optional ones. Please refer to each individual pipeline's documentation page in this wiki to get a full list of available parameters and acceptable values for each.

#!bash

#database config parameters
host=localHost
user=sqlite
password=sqlite
DB=/tempFileDir/outputDir/DBFile.db
DBtype=sqlite

#Java arguments
Xmx=500G

#CreateHaplotype Params
referenceFasta=/path/to/reference/ref.fasta
LoadHaplotypesFromGVCFPlugin.keyFile=/path/to/keyfile/keyFile.txt
LoadHaplotypesFromGVCFPlugin.gvcfDir=/path/to/gvcfs/
LoadHaplotypesFromGVCFPlugin.referenceFasta=/path/to/reference/ref.fasta
LoadHaplotypesFromGVCFPlugin.haplotypeMethodName=GATK_PIPELINE
LoadHaplotypesFromGVCFPlugin.haplotypeMethodDescription=GVCF_DESCRIPTION

#Haplotype filtering
mapQ=48
DP_poisson_min=.01
DP_poisson_max=.99
GQ_min=50
filterHets=t

#sentieon license
sentieon_license=cbsulogin2.tc.cornell.edu:8990

#Consensus parameters
#Optional argument to get out merged VCF files for debugging consensus
includeVariants=true
mxDiv=.001
maxError=0.2

#FindPath Config parameters
BestHaplotypePathPlugin.maxNodes=30
BestHaplotypePathPlugin.minTaxa=5
BestHaplotypePathPlugin.minReads=1
BestHaplotypePathPlugin.maxReads=100
BestHaplotypePathPlugin.minTransitionProb=0.001
BestHaplotypePathPlugin.probCorrect=0.99
BestHaplotypePathPlugin.splitNodes=true
BestHaplotypePathPlugin.splitProb=0.99