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

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.

snp
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updated by Kevin Blighe Kevin Blighe • written by jinxinhao1988 jinxinhao1988

What you want is an allele frequency threshold.

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

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written by h.mon h.mon

1 answer

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

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written by Kevin Blighe Kevin Blighe

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