Hi, I would like to calculate absolute allele frequency differences (delta) for each SNPs of two populations (using 1000 genomes vcf data). I could not find the correct formula for this. Could anyone tell me how to do?
The delta Allele Frequency is just the difference of the frequencies of the allele in the two populations. However, to calculate it, you must first choose which allele to use to calculate the frequency: the derived allele. If you know which is the ancestral allele, you can calculate the delta DAF. Otherwise, the deltaMAF is fine for most cases.
- absoluted delta Derived Allele Frequency (deltaDAF) -> frequency of the most recent allele (not the Ancestral Allele)
- absolute delta Minor Allele Frequency (deltaMAF) -> frequency of the allele that has the minor frequency in a reference population (e.g. in CEU).
1000 Genomes already provides an annotation on which is the minor allele (see the VCF file).