the formula which calculate the rate of heterozygosity in kmer analysis

Question

[70910595]

I want to calculate the rate of heterozygosity in kmer analysis。 I tried to use some software like BBMAP ,genomecope,gce.. But the results were not satisfactory。。 So，I want to know how could i calculate the rate of heterozygosity by myself。

Thank you for your help!

Answer 1

[Brian Bushnell]

You can calculate the het rate of a diploid, approximately, like this:

Where K is the kmer length, A is the number of unique kmers in the first (1-copy) peak and B is the number of unique kmers in the second (2-copy) peak, and G is the haploid genome size:

hetRate=(A/K)/G

The genome size can be approximated by:

G=A/2+B

You can add the first repeat peak (4-copy) into the genome size with an extra term "+2*C", and so forth for higher copy peaks, but that typically doesn't have much effect.

[fgajardoe]

i just want to make sure, K is k-mer size?

[Brian Bushnell]

Yes, that's correct. I'll edit my answer.