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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
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