# Imputation Pipeline parameters for VCF files

#!!! Required Parameters !!!
#--- Database ---
host=localHost
user=sqlite
password=sqlite
DB=**UNASSIGNED**
DBtype=sqlite

#--- Used by liquibase to check DB version ---
liquibaseOutdir=/phg/outputDir

#--- Used for indexing SNP positions ---
#   pangenomeHaplotypeMethod is the database method or methods for the haplotypes to which SNPs will be indexed
#   the index file lists the SNP allele to haplotype mapping and is used for mapping reads
pangenomeHaplotypeMethod=**UNASSIGNED**
indexFile=/phg/outputDir/vcfIndexFile
vcfFile=/phg/inputDir/imputation/vcf/yourFilenameHere.vcf

#--- Used for mapping reads
#   readMethod is the method name for storing the resulting read mappings
#   countAlleleDepths=true means allele depths will be used for haplotype counts, which is almost always a good choice
inputType=vcf
keyFile=/phg/readMapping_key_file.txt
readMethod=**UNASSIGNED**
vcfDir=/phg/inputDir/imputation/vcf/
countAlleleDepths=true

#--- Used for path finding
#   pathHaplotypeMethod determines which haplotypes will be consider for path finding
#   pathHaplotypeMethod should be the same as pangenomeHaplotypeMethod, but could be a subset
#   pathMethod is the method name used for storing the paths
pathHaplotypeMethod=**UNASSIGNED*
pathMethod=**UNASSIGNED*
maxNodes=1000
maxReads=10000
minReads=1
minTaxa=20
minTransitionProb=0.001
numThreads=3
probCorrect=0.99
removeEqual=true
splitNodes=true
splitProb=0.99
usebf=false
maxParents = 1000000
minCoverage = 1.0
#parentOutputFile = **OPTIONAL**

#--- used by haploid path finding only
#   usebf - if true use Forward-Backward algorithm, other Viterbi
usebf=false
minP=0.8

#--- used by diploid path finding only
maxHap=11
maxReadsKB=100
algorithmType=efficient

#--- Used to output a vcf file for pathMethod
outVcfFile=**UNASSIGNED**

#~~~ Optional Parameters ~~~
#readMethodDescription=**OPTIONAL**
#pathMethodDescription=**OPTIONAL**
#bfInfoFile=**OPTIONAL**
#~~~ providing a value for outputDir will write read mappings to file rather than the PHG db ~~~
#outputDir=**OPTIONAL**