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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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Rank of eigen matrix <=1 #15

Open JoniColeman opened 1 year ago

JoniColeman commented 1 year ago

Hi,

Issue: I am running DENTIST_1.2.0.0 (pre-compiled) on GWAS summary statistics for height (2018 meta-analysis if you want to reproduce, with 1000G EUR samples as an LD reference). In general, everything works fine, but when I run it for chr11 it fails with the error message: [error] Rank of eigen matrix <=1. I have mapped the issue to the centromere of the chromosome (somewhere between 47Mb and 52Mb on build 37).

Could you explain a little what is causing this error in DENTIST? Do you have any suggestions for what I could do to fix it?

Thank you in advance

Yves-CHEN commented 1 year ago

This message means that the pseudo inversion of the LD matrix failed. This could be that SNPs in the region( 47Mb and 52Mb) is very sparse or is very correlated. A quick solution is to identify the problematic region (very likely a gap region) and leave it out by dividing the GWAS summary.