i just want to make sure, K is k-mer size?
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!
1 answer
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.
Yes, that's correct. I'll edit my answer.
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