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Yves-CHEN / DENTIST

DENTIST (Detecting Errors iN analyses of summary staTISTics) is a QC tool for summary-data-based analyses.
GNU Lesser General Public License v3.0
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[error] LD was set to 0 #5

Closed privefl closed 4 years ago

privefl commented 4 years ago

For some chromosomes, I get the following error:

dentist_error

Any idea where it comes from?

Yves-CHEN commented 4 years ago

Hi. This happens when the reference has NA genotypes. If this is the case for you, please add --with-NA-geno flag when running DENTIST, which should fix this. Also please note that for good QC performance, a reference sample should be >5000 in sample size, and conventional QC are applied (e.g. HWE, MAC>5).

privefl commented 4 years ago

I don't seem to have this issue anymore with the new version. But I don't think I had any missing values in the genotypes.