How to use mutation rate to identify a homozygous or heterozygous mutation?

Question

[jinxinhao1988]

Dear all,

I have a question that we use software to call SNP, and get the mutation rate of each SNP, are there any standards to identify if it is a homozygous mutation? like setting a threshold of 40%-80% is heterozygous mutation, and beyond 80% or beneath 40% is homozygous mutation. If there is a international recognized standard?

Thank you for your time.

[h.mon]

What you want is an allele frequency threshold.

Mutation rate is the frequency of nucleotide base changes (new mutations) as time passes.

Answer 1

[Kevin Blighe]

There is definitely no international standard for this. Standards are lacking in bioinformatics. Equally, different variant callers will have different thresholds. I've seen thresholds for homozygous at 80 or 90%, whilst, for heterozygous, I've seen the figure at usually 40%:60% split. However, in one case, I saw a pipeline where the analysis methods were so poor that they reduced the heterozygous calling rate to 10%:90%, which is obviously non-sensical if you equally want to call homozygous faithfully.

Kevin