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perslab / depict

DEPICT code, instructions and an example
GNU General Public License v3.0
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Number of permutation files are insufficient #13

Closed ZKamali closed 5 years ago

ZKamali commented 5 years ago

Dear Tune H Pers, Number of precomputed loci (permutation files) are usually less than what is specified in configuration file (.cfg). for example when we specify 500 it generates 495. Interestingly in all cases these missing files are the same! (i.e "permutation57.txt.gz", "permutation69.txt.gz", "permutation71.txt.gz", "permutation171.txt.gz" and "permutation182.txt.gz"). Please let us know how to fix this problem.

ZKamali commented 5 years ago

I figured out. its because of presence of minus values for P in some of the null gwas files which prevents plink to do clumping.