<p>Hi, thanks for taking the time. I am learning Plink these days and find one question. I download the example(called hapmap) in the website and find the number of genotype data in the PED is different from the number of SNP in the MAP. I want to know if anyone knows the reason. Thanks a lot.</p>

How did you count the genotype data in the PED?

The PED has SNPs for columns and individuals for rows (2 columns per SNP! I.e., `A   A` instead of `AA`), while the MAP has SNPs as rows. Furthermore, the first few columns in a PED file are not genotypes - they are

```
Family ID
Individual ID
Paternal ID
Maternal ID
Sex (1=male; 2=female; other=unknown)
Phenotype
```

[Source][1]

Therefore,

    wc -l your_map_file.map

should be identical to

    awk '{print (NF - 6)/2}' your_ped_file.ped | head -1

The first wc command prints the number of lines in the map file (= number of SNPs in map), the second prints the number of columns (NF) minus the 6 additional IDs, divided by 2 since you always have two columns per SNP.

If your numbers are actually different, try re-downloading the files.

 [1]: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml