FAPI: Fast and Accurate P-values imputation for genetic association

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.
ImputePValue The imputed p-value
Confidence The (1-variance) of the conditional normal distribution on which the imputation was carried out. It ranges from 0 to 1. The larger the better. The cut-off 0.4 is recommended.
ProbC The probability of the observed p-value is equal to the imputed p-value. In principle, it is measured by by Prob(Z>=the corresponding z score of the observed p-value ) if the z score is over the mean of the conditional normal distribution; otherwise 1-Prob(Z>=the corresponding z score of the observed p-value ).

The smaller ProbC the less likely the observed p-value is supported by its nearby SNPs in high LD. For whole genome data, the cutoff ProbC, 1E-6 is recommended.

Note when the confidence score is low say < 0.6, the ProbC will be not calculated. A '.' will appear.

Miao-xin Li, Jia-en Deng, Center for Genomic Sciences & Department of Psychiatry, The University of Hong Kong, All rights reserved.