I don't have vcf file. I rsid/snp id, chrom, position, growth parameters, case n control. Quality control, HWE, logistic regression.
Sorry, I would like to perform in Plink. The question is to generate .bed, .map. .fim files from csv files having Marker, variety and phenotype information. How will I separate case and control or should case and control in one file.
I have phenotype and genotypic information for each marker. The information is like this:
PATIENT MARKER ALLELE1 ALLELE2 CHROM DIST Sowing Disease PLACE XX Seed Pod Length UREA
SWS1 RS55514 G G 7 28028432 2016-04-17 LR UP 1 79 1 9.3 6
SWS2 RS55514 A G 7 28028432 2017-10-11 YR MP 1 72 1 6.5 6
SWS3 RS55514 G G 7 28028432 CH 1 65 1 12 6
Thank you. I prepared .ped and .map file, Now I would like to calculate Odds ratio, MAF, pvalue for each marker. When I executed the command
plink --file Wei --assoc --maf 0.05 --out run1
I got NA in Odds ratio column.
Simultaneously I have to predict Odds ratio and pvalue for each environmental factor or clinical factors for particular SNP.
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