configfile_eQTL.yaml

#==================================== 
## Sample configuration file for Fine mapping eQTLs using FINEMAP
#==================================== 

##=============
## fine mapping related parameters
##=============
Finemap:
  ## type of fine-mapping - eQTL / GWAS - keep the entry as it is
  Study: "eQTL"
  ## number of causal SNPs to be tested for fine mapping
  ## better to keep it as it is
  NUMCAUSALSNP: 10
  ## number of threads to be used
  NUMTHREAD: 8

##=============
## various parameters related to paths / executables
##=============
Path:
  ## output directory to store the fine mapping results
  OutDir: "/home/sourya/finemap_out"
  ## ldstore executable
  ## check LDSTORE2 from http://www.christianbenner.com/
  ldstoreexec: "/home/sourya/ldstore_v2.0_x86_64"
  ## finemap executable
  ## check FINEMAP from http://www.christianbenner.com/
  finemapexec: "/home/sourya/finemap_v1.4_x86_64"
  ## directory storing 1000G data
  ## PLINK formatted files
  GENOTYPEDIR: "/home/sourya/genomes/1000G_Phase3_Genotype/ALL"
  ## Number of samples for this genotype data
  ## check the file "all_phase3.psam" in the parent directory (wc -l) to see the number of samples
  ## for 1000G reference genotye (hg19), this is the sample size, and user does not need to change this parameter.
  samplecount: 2504

##=============
## various parameters related to eQTLs (summary statistics)
##=============
Stat:
  ## input eQTL summary statistics file
  Filename: "Data/Example_eQTL_data.txt"
  ## column containing the chromosome name
  chrCol: 1
  ## SNP position
  posCol: 2
  ## column containing the gene ID (mandatory parameter)
  geneIDCol: 3
  ## column containing the gene name
  geneNameCol: 11
  ## SNP rsID column
  rsIDCol: 4
  ## column containing the p-value
  pValCol: 5
  ## column containing the beta
  ## Note: either "betaCol" or "ORCol" needs to be provided
  betaCol: 7
  ## column containing the odds ratio
  ## mandatory if beta statistics is not provided
  ## otherwise, can be empty
  ORCol: 
  ## column containing the allele frequency information
  ## if not provided, the fine mapping code inserts a dummy minor allele frequency - say 0.1  
  AFCol: 
  ## column containing the standard error
  SECol: 
  ## column containing sample size  
  SampleSizeCol:
  ## total sample size (an integer) if specified
  TotalSample: 91