GEC (v.0.2)- Genotype Error 1 software is used to calculate the number of independent SNPs. As far as I know, it requires the genotype file to be in bed format.
Li MX, Yeung JM, Cherny SS, Sham PC. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum Genet. 2012 May;131(5):747-56. doi: 10.1007/s00439-011-1118-2. Epub 2011 Dec 6. PMID: 22143225; PMCID: PMC3325408.
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