CORR_TOO_HIGH

[fatma.b...@gmail.com]

Hi Chris,

I have tested the associations of different SNPs by using (--linear genotypic) command. However for some SNPs I got the the error (CORR_TOO_HIGH). Then I have checked the frequency of the different genotypes of a SNP that gave this error. We can see that some genotypes were either not present = 0 or occurs only once (Please find attached photo).

Is this the reason that I get the error. And how can I tackel this problem? can I still use the (--linear genotypic) command and get a p-value, or not?

Best regards,

Fatma Mokhtar

[Christopher Chang]

I added the following to the 'genotypic'/'hethom' online documentation last week, in response to your previous question:

"Note that these two modifiers only make sense when analyzing variants with fairly high MAF. Otherwise, you are very likely to get a 'NA' result, since there are too few homozygous-minor genotypes to reliably distinguish the additive and dominance-deviation effects from each other."