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Common variants (MAF ≥ 5%) calling

• Minor allele frequency (MAF) is the frequency at which the second most common allele occurs in a given population. MAF is widely used in population genetics studies because it provides information to differentiate between common, low-frequency and rare variants in the population.

#NOTE: Common (MAF ≥ 5%), low-frequency (0.5 ≤ MAF ≤ 5%) and rare (MAF ˂ 0.5%) variants.

plink --bfile Workshop_samples_05-17-23_nocont_homo --maf 0.05 --make-bed --out Workshop_samples_05-17-23_nocont_homo_common

#NOTE: Download the Workshop_samples_05-17-23_nocont_homo_common.bim , open it in excel and save it as common_variants.

6. Functional analysis

./mutserve annotate --input variantsfile.txt --annotation rCRS_annotation_2020-08-20.txt --output AnnotatedVariants.txt

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