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Old 12-03-2015, 03:07 AM   #1
RonanWhiston
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Location: Ireland

Join Date: Feb 2013
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Default Genomic Inflation Factor Less than 1 in GenABEL

Hi,

I've re-sequenced whole-exomes of 24 bulls, performed SNP calling using GATK HaplotypeCaller and performed an association of SNP genotypes with a fertility phenotype.

I calculated the genomic inflation factor, the genomic inflation factor (lambda) is defined as the ratio of the median of the empirically observed distribution of the test statistic to the expected median, thus quantifying the extent of the bulk inflation and the excess false positive rate.

However, my lambda score is 0.8, less than 1. Inflated (lambda) values or residual deviations in the QQ plot may point to undetected sample duplications, unknown familial relationships, a poorly calibrated test statistic, systematic technical bias or gross population stratification.

What does it mean to have a reduced lambda value?

Thanks to anyone who can help,
Ronan
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