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swvanderlaan / MetaGWASToolKit

A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies
https://swvanderlaan.github.io/MetaGWASToolKit/
MIT License
15 stars 2 forks source link

Clumps are 'cleared' #3

Closed swvanderlaan closed 6 years ago

swvanderlaan commented 6 years ago

For some reason parseClumps.pl literally 'greps' the contents of *.clumped-files, so essentially the contents are cleared. It is not really a problem, the contents are parsed and printed to a new file, but ideally the original results should be kept in the input-files (i.e. *.clumped-files).

swvanderlaan commented 6 years ago

This is a fluke. Somehow, when there are many columns indicated using --clump-annotate the results and these annotations are shifted to the right by PLINK v1.9.