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The data is present in the PLINK format .bed (individual genotypes), .bim (genetic markers) and .fam (sample IDs and disease phenotype file). I have also separate text files containing information on subjects related to two populations. (i.e. European and Hispanic)

Question related PLINK data

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  1. You need to report allele frequencies using plink for some European samples
  2. Do the same for Hispanic samples
  3. Use a software to subtract the two allele frequencies obtained above and obtain the result.
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  • $\begingroup$ Hi, I think I kind of understood what you mean. So in PLINK, we use --freq command to find information on frequency. and what software do you recommend to subtract the frequency files of two populations? thank You $\endgroup$
    – Amara
    Commented Apr 22, 2020 at 2:50

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