Links of MX Li's tools:
 

Validate association p values at typed SNPs 
options 

1) Validate p values for genetic association by haplotype reference data in VCF format or PLINK format 

java Xmx3g jar fapi.jar qc pfile ./plink.assoc.hg19.txt gfile hapmapr22::vcf
java Xmx3g jar fapi.jar qc pfile ./plink.assoc.hg19.txt gfile test::plink

Hint: If the reference genotypes are stored in different files chromosome by chromosome,
you can use _CHROM_ to denote the chromosome names [1...Y] in the file name.
e.g. chr_CHROM_.phase1.cvf.chinese. 

Output: 


Description 
.... 

ImputePValue 
The imputed pvalue 
Confidence 
The (1variance) of the conditional normal distribution on which the imputation was carried out. It ranges from 0 to 1. The larger the better. The cutoff 0.4 is recommended. 
ProbC 
The probability of the observed pvalue is equal to the imputed pvalue. In principle, it is measured by by Prob(Z>=the corresponding z score of the observed pvalue ) if the z score is over the mean of the conditional normal distribution; otherwise 1Prob(Z>=the corresponding z score of the observed pvalue ).
The smaller ProbC the less likely the observed pvalue is supported by its nearby SNPs in high LD. For whole genome data, the cutoff ProbC, 1E6 is recommended.
Note when the confidence score is low say < 0.6, the ProbC will be not calculated. A '.' will appear.


Miaoxin Li, Jiaen Deng, Center for Genomic Sciences & Department of Psychiatry, The University of Hong Kong, All rights reserved. 