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 It is preserved here for archival and historical reference only.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

Sample Config file for Loading Haplotypes.

To Load haplotypes a config file will be needed. Here is a sample one with most of the needed information filled out. Anything marked with UNASSIGNED will need to be updated with a correct value and anything OPTIONAL is optional and depending on your use should be removed.

#!

###Example config file. 
### Anything marked with UNASSIGNED needs to be set for at least one of the steps
### If it is marked as OPTIONAL, it will only need to be set if you want to run specific steps. 
host=localHost
user=sqlite
password=sqlite
DB=/phg/smallSeqDB.db
DBtype=sqlite

#System parameters.  Xmx is the java heap size and numThreads will be used to set threads available for multithreading components.
Xmx=10G
numThreads=10

liquibaseOutdir=/phg/outputDir

anchors=***UNASSIGNED***
genomeData=***UNASSIGNED***

referenceFasta=***UNASSIGNED***

asmMethodName=mummer4
asmKeyFile=***OPTIONAL***

wgsMethodName=GATK_PIPELINE
wgsKeyFile=***OPTIONAL***

consensusMethodName=CONSENSUS
inputConsensusMethods=GATK_PIPELINE

fastqFileDir=/phg/inputDir/loadDB/fastq/
dedupedBamDir=/phg/inputDir/loadDB/bam/dedup/

gvcfFileDir=/phg/inputDir/loadDB/gvcf/
filteredBamDir=/phg/inputDir/loadDB/bam/mapqFiltered/

# BAM and GVCF uploading parameters
mapQ=48
refRangeMethods=FocusRegion,FocusComplement
extendedWindowSize=1000

# WGS Haplotype Filtering criteria.  These are the defaults.
GQ_min=50
QUAL_min=200
DP_poisson_min=.01
DP_poisson_max=.99
filterHets=true

## If you have a sentieon license you can set the server location here(and remove the #).  If it is set, it will use Sentieon instead of GATK
#sentieon_license= ***OPTIONAL***


##Consensus Plugin Parameters
minFreq=0.5
maxClusters=30
minSite=30
minCoverage=0.1
maxThreads=10
minTaxa=1
mxDiv=0.01

#This sets the type of clustering mode.
#Valid params are: upgma, upgma_assembly, and kmer_assembly
#The two assembly parameters are designed for assembly haplotypes and will choose a representative haplotype as the consensus instead of attempting to merge calls like with upgma.
clusteringMode=upgma

#If you want to use an assembly clusteringMode, you must have a ranking file.
#The ranking file must be a tab separated list of taxon\trankingScore where higher numbers are a better rank.  This file is used to chose the representative haplotype
rankingFile=***OPTIONAL***

##Optional if you want to use kmer_assembly as the clusteringMode. Otherwise is ignored 
kmerSize=7
distanceCalculation=Euclidean