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ANGSD / angsd

Program for analysing NGS data.
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What is PPmaf? #578

Open shirasegoby opened 1 year ago

shirasegoby commented 1 year ago

Hi,

Thank you for developing this great software. I would like to calculate minor allele frequencies in each locus and did it using -doMaf 4 and beagle file. I understand that PPmaf is minor allele frequency, but a few PPmaf is over 0.5. So, my question is below.

  1. PPmaf is a minor allele frequency. Is this correct?
  2. Why do a few SNP loci show over 0.5 minor allele frequency?

Best,

beausoleilmo commented 7 months ago

I'm seeing the same thing with my beagle file. Don't know why this is the case.