#database config parameters
host=localHost
user=sqlite
password=sqlite
#DB=/tempFileDir/outputDir/Cassava_HMIII.db
DB=Cassava_HMII_V3_Marning_imputation_6-18-21.db
DBtype=sqlite
#referenceFasta=/tempFileDir/data/reference/cassavaV7_chrAndScaffoldsCombined_numeric.fa
referenceFasta=/workdir/eml255/Cassava_PHG_Het/Reference/cassavaV6_chrAndScaffoldsCombined_numeric.fa
#Java arguments
Xmx=100G
#LoadHaplotypesFromGVCFPlugin.wgsKeyFile=/tempFileDir/data/keyFile.txt
#LoadHaplotypesFromGVCFPlugin.gvcfDir=/tempFileDir/data/outputs/gvcfs/
#LoadHaplotypesFromGVCFPlugin.haplotypeMethodName=GATK_PIPELINE
#LoadHaplotypesFromGVCFPlugin.haplotypeMethodDescription="Senteon IBD haplotypes"

#Haplotype filtering
mapQ=48
DP_poisson_min=.05
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
exportMergedVCF=/tempFileDir/data/outputs/mergedVCFs/
includeVariants=true
mxDiv=.001
numThreads=20
maxError=0.2
useDepth=false
replaceNsWithMajor=false
method=upgma
minTaxa=1

#FindPath Config parameters
includeVariantContexts=true
maxNodesPerRange=30
minTaxaPerRange=1
minReads=0
maxReadsPerKB=5000
minTransitionProb=0.001
probCorrect=0.95
emissionMethod=allCounts
splitTaxa=false