Question: Calculate Allele Frequency from PLINK PED/MAP files
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shahil229.sa • 0 wrote:
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
Thank you for your time.
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.