I am reading a paper that is about a software tools VarScan2.
In that context, There is a sentence that I don't understand. Below is the sentence.
By default, VarScan2 require minimum coverage of 3X, minimum phread base quality of 20, allele frequency of at least 8% and P-value of < 0.05. Variants with a variant allele frequency of >75% are called homozygous.
I don't understand that why allele frequency greater than 75% becomes homozygous?
and How can I decide the homo and het considering only the allele frequency?
Is there any feature of characteristic that decide the homo or het regarding the allele frequency?
(I already know the simple concept of allele frequency. I searched the wiki and got it what it means)
It's very confused concept for me to understand allele frequency connected to nucleotide base level.
I think it might be easy for you because i have not much backgrounds in genetics.
I hope you understand !
I am looking forward to your a reply.