Hello All,
I have .bed/.bim/.fam files and .pgen/.psam/.pvar files with me How to calculate GWAS Summary Statistics? which data files are useful?
Desired Output:
CHR BP SNP A1 A2 N SE P OR INFO MAF
1 756604 rs3131962 A G 388028 0.00301666 0.483171 0.997886915712657 0.890557941364774 0.369389592764921
2 768448 rs12562034 A G 388028 0.00329472 0.834808 1.00068731609353 0.895893511351165 0.336845754096289
9 779322 rs4040617 G A 388028 0.00303344 0.42897 0.997603556067569 0.897508290615237 0.377368010940814
Where:
CHR: The chromosome in which the SNP resides
BP: Chromosomal co-ordinate of the SNP SNP: SNP ID, usually in the form of rs-ID
A1:The effect allele of the SNP A2: The non-effect allele of the SNP
N: number of samples used to obtain the effect size estimate
SE: The standard error (SE) of the effect size estimate
P: The P-value of association between the SNP genotypes and the base phenotype
OR: The effect size estimate of the SNP, if the outcome is binary/case-control. If the outcome is continuous or treated as continuous then this will usually be BETA
INFO: The imputation information score
MAF: The minor allele frequency (MAF) of the SNP
