Step-by-Step Guide to Minor Allele Frequency (MAF) Calculation

Introduction to Minor Allele Frequency

• Definition: Minor allele frequency (MAF) is the proportion of the second most common allele (the minor allele) in a given population.
• Importance:
  • Helps identify genetic variants associated with diseases.
  • Used in genome-wide association studies (GWAS) and population genetics.
  • Helps understand evolutionary patterns and genetic diversity.
• Applications:
  • Medical Research: Identifying rare genetic variants in diseases.
  • Population Studies: Examining diversity among populations.
  • Pharmacogenomics: Tailoring drugs based on genetic variations.

Step 1: Understand the Basics of Allele Frequencies

• Each individual in a diploid organism has two alleles for a SNP (Single Nucleotide Polymorphism).
• If the population size is $N$:
  • Total number of alleles = $2\times N$.
• If the major allele frequency (e.g., $A$) is $0.6$, the minor allele frequency (e.g., $G$) is $1-0.6=0.4$.

Step 2: Manual Calculation

Suppose you have a SNP with the following data:

• Population size = 100 individuals.
• Major allele (A) = 0.6.
• Minor allele (G) = 0.4.

Steps:

1. Total alleles = $100\times 2=200$.
2. Number of $G$ alleles = $200\times 0.4=80$.
3. Verify:
   • $A$ alleles = $200\times 0.6=120$.
   • Total alleles = $80+120=200$.

For a minor allele frequency of $0.05$:

• $\text{Number of minor alleles}=200\times 0.05=10$.

Step 3: Using Databases

For larger datasets or known SNPs:

1. NCBI dbSNP: Provides allele frequencies across populations.
   • URL: NCBI dbSNP
2. 1000 Genomes Project: Offers population-based MAF data.

Step 4: Automating the Calculation with UNIX and Perl

UNIX Approach

If you have a VCF (Variant Call Format) file:

1. Extract Allele Counts:
   bash

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   bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO/AF\n' input.vcf > allele_frequencies.txt

   • AF represents allele frequency.
2. Filter for MAF < 0.05:
   bash

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   awk '$5 < 0.05' allele_frequencies.txt > rare_variants.txt


Perl Script

If you have a tab-delimited file with allele counts:

1. Save the file as calculate_maf.pl.
2. Run the script:
   bash

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   perl calculate_maf.pl


Step 5: Validation

Verify results using population genetics tools:

• PLINK: Compute allele frequencies and filter based on MAF.
  bash

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  plink --vcf input.vcf --freq --out allele_frequencies


Conclusion

By understanding and automating MAF calculations, researchers can efficiently analyze SNP data for diverse applications. Tools like bcftools, awk, and PLINK, combined with manual validation, provide robust workflows for both small and large datasets.