Info Score > 1 Plink?

Question

[bg1116]

What does an info score > 1 mean? I thought all scores should be between 0 and 1. Info score comes from assoc.dosage file in plink.

[Kevin Blighe]

did you check the plink manual pages:

The fields INFO and NPRX refer to how well PLINK managed, if at all, to impute the SNP. If NPRX is zero, then it could not be even poorly imputed. If INFO ranges from between 0 and 1, although it can be greater than 1 occasionally. A higher value general means a better imputed SNP; roughly speaking, only looking at imputed SNPs with a INFO value greater than 0.8 or so is probably good practice. More specific details on these metrics will be posted soon.

...I put in bold the important line.

Kevin

[chrchang523]

INFO has the same meaning in both files, but that documentation snippet is actually for a slightly different (and defunct) command, --proxy-assoc instead of --dosage.

Answer 1

[chrchang523]

The INFO field in an .assoc.dosage file contains the MaCH r-squared imputation quality metric, which is [observed dosage variance] / [expected variance, given observed allele frequencies and Hardy-Weinberg equilibrium]. Despite the r-squared name, this is not guaranteed to be less than or equal to 1, especially when there's significant deviation from Hardy-Weinberg equilibrium; but low values can still be trusted to correspond to poorly-imputed SNPs.

[curious]

When performing association tests on dosage data, it looks like my poorly imputed variants (Rsq < .3ish) get NA pvalues. I would usually filter those out anyways, but out of curiosity is there an internal cutoff in PLINK that excludes sites with low Rsq from the test?