Minor Allele Frequency Cutoff/Threshold

[BertieWooster]

G'day,

I am writing to enquire what maf cutoff/threshold people use when getting snps using the maq snp caller or any other means.

A lot of researchers seem to use 0.05 as applied for HapMap, but this is applicable for population data. Is there a "statistical" way to estimate this from the data or should one just do it arbitrarily?

Cheers!
BertieWooster

[jaspersaris]

Hai Bertie,
I am not sure what you mean. In a normal, autosomal, say recessive disease like situation I place my cutoff at 20%. That's based on Sangerseq based views and clean sequences in Seqscape. In situations were we aware of possible mosaic situations we first improve our sequences and then can pickup at 5-10%. So 0.05 in a none optimised sequenceproject is probable generating false-positives. I haven't explored/realised it yet, but yes, by counting each variant per base and having enough seq-depth would yield a cluster and borders there-off to estimate a general or floating statistics based cutoff.
Regards, Jasper