Calculate Allele Frequency from PLINK PED/MAP files
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6.6 years ago

Hi, I am completely new to genetics and i have minimal understanding about this topic. For a university project I have to program a few genetic tests to run on PLINK PED/MAP files in java. I am having a tough time understanding how I can use the information from the PLINK files to calculate Allele Frequencies of mutations. If someone could please help I would be eternally grateful.

PED file given

CEU1463 1 0 0 0 -9 G G C C C T T T G G A G A A T T T C G G A A A G C T C C A A G A G A C G A A C G A A G G T C G G C C T G A T A C T T G G A G
CEU1463 2 0 0 0 -9 G G G C T T C T G G G G G A A T C C T T G G G G C T A C A A A A A A G G G A G G G A T G C C A G C C G G T T A C G T G G A G
CEU1463 3 1 2 0 -9 G G G C C T T T G G G G G A T T T C G T G A G G C T A C A A A A A A C G G A G G G A G G T C G G C C G G A T C C G T G G A G

MAP file given

1	rs986032	0	168549668
1	rs1840312	0	189435808
1	rs34623224	0	216209037
2	rs10164413	0	7990067
2	rs1523817	0	200312090
4	4:132693617	0	132693617
4	rs12500154	0	137957327
4	rs6858105	0	172347711
5	rs1366437	0	27971560
5	rs629148	0	73878444
5	rs2409539	0	127847321
6	rs11964920	0	25343760
6	rs3025010	0	43855555
6	rs9384362	0	156175324
7	rs7778281	0	133988239
9	rs12379608	0	134602550
10	rs7896657	0	5034291
11	rs2255200	0	6341649
11	rs643281	0	101891286
11	rs11221484	0	128244665
12	rs7302076	0	32126500
12	rs224589	0	49685317
13	rs7999581	0	64029283
14	rs743221	0	62927561
14	rs10137314	0	100279487
15	rs11072197	0	68577103
17	rs11870955	0	69868079
18	rs12964535	0	31865689
18	rs12604865	0	75211701
19	rs12610631	0	1865535
19	rs10421861	0	49042947

SNP allele frequency plink ped map • 3.7k views
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Read the documentation of PLINK files. PED file has in rows SNPs, and in columns with alleles individuals (2 alleles per individual). When you calculate MAF or just allele frequencies with plink it shows for given SNP those frequencies.
You find which variant you consider a mutation, and get the frequency of that allele for the SNP.