How is the overall “AGVD” allele frequency calculated?

Only the cohorts considered to be predominantly of African ancestry were used to calculate this frequency. This means that ASW and ACB were included even though those samples were not collected on the African continent

The variant I’m looking for does not appear in the results.

  • Try searching by location (e.g. 20:300000-400000)
  • If the variant is still not found this could be due to:
    • It having been filtered out in the joint calling
    • The variant being REF/REF for all of the samples

The variant I’m looking at shows an “AGVD” frequency of zero. Why is it in the data?

  • The “AGVD freqeuncy” reported is calculated from samples with African ancestry
  • This would happen if the alt allele was only observed in non African samples in the joint-called data. This can be confirmed by looking at the detailed cluster frequencies.