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vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis
https://vatlab.github.io/vat-docs/
GNU General Public License v3.0
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KING version 2.1.4 and 2.2.4 different results #130

Closed gaow closed 5 years ago

gaow commented 5 years ago

Here is the analysis of notebook on #120 using KING version 2.2.4:

Screenshot from 2019-10-28 00-23-13

and here, using version 2.1.4:

Screenshot from 2019-10-28 00-23-33

KING.pipeline between these 2 versions are also slightly different due to output format change btw these 2 KING versions ...

gaow commented 5 years ago

I just investigated into this some more. Turns out version 2.1.4 and 2.2.4 are the same (except for a sign flip in PC1) and also agrees with version 1.4. The difference above was because different variant tables were used. This is a relief. I have now finalized KING.pipeline for version 2.2.4.