parameters.csv

##DEFAULT DIRECTORY PARAMETERS
workDir,/groups/${group}/${tmpDir}/generatedscripts/
dataDir,/apps/data/
tempDir,/groups/${group}/${tmpDir}/temp
projectDir,/groups/${group}/${tmpDir}/projects/${study}/${run}/


##LIFTOVER PARAMETERS
liftOverInputFile,${workDir}/${study}/${rawdata}/chr${chr}
liftOverChainFileDir,${dataDir}/chainFiles/


##PHASING PARAMETERS
geneticMapPhasing,${dataDir}/www.shapeit.fr/genetic_map_b37/genetic_map_chr${chr}_combined_b37.txt


##GENOTYPEHARMONIZER PARAMETERS
pathToReference1000G,${dataDir}/${referenceGenome}/phase1/GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL/chr${chr}.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz
pathToReferenceGoNL,${dataDir}/${referenceGenome}/release5_noContam_noChildren_with_AN_AC_GTC_stripped/gonl.chr${chr}.snps_indels.r5.vcf.gz
pathToReferenceHRC,/groups/umcg-lifelines/tmp03/EGAD00001002729/EGAZ00001239293_HRC.r1-1.EGA.GRCh37.sites.vcf.gz


##IMPUTATION PARAMETERS
pathToPhasedReference1000G,${dataDir}/${referenceGenome}/imputationReference_phased_b37/ALL_${referenceGenome}_phase1integrated_v3_chr${chrom}_impute
pathToPhasedReferenceGoNL,${dataDir}/${referenceGenome}/imputationReference_phased_b37/chr${chrom}
pathToPhasedReferenceHRC,/groups/umcg-lifelines/tmp03/EGAD00001002729/
geneticMapImputation,${dataDir}/www.shapeit.fr/genetic_map_b37/genetic_map_chr${chrom}_combined_b37.txt


##CONCATCHUNKS PARAMETERS
concatChunksFile,${intermediateDir}/chr${chrom}_concatenated
concatChunksInfoFile,${intermediateDir}/chr${chrom}_info_concatenated


##COPYTORESULTSDIR PARAMETERS
liftOverResultsDir,${projectDir}/results/liftOver/
logsResultsDir,${projectDir}/results/logs/
finalResultsDir,${projectDir}/results/finalResults/


##TMP FOLDERS
intermediateDir,/groups/${group}/${tmpDir}/tmp/${study}/
outputPerChr,${intermediateDir}/chr${chr}
outputPerChunk,${intermediateDir}/chr${chrom}_${fromChrPos}-${toChrPos}


##MODULE VERSIONS
pipelineVersion,Imputation/1.0.0
plinkVersion,plink/1.9-foss-2015b
liftOverUcscVersion,liftOverUcsc/20161011
shapeItVersion,shapeit/v2.r837-static
genotypeHarmonizerVersion,GenotypeHarmonizer/1.4.18-Java-1.8.0_45
imputeVersion,IMPUTE4/r265.2
qctoolVersion,qctool/1.4
pigzVersion,pigz/2.3.1-foss-2015b