FAPI: Fast and Accurate P-value Imputation for genetic association
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Miaoxin Li

Links of MX Li's tools:

 
Impute p-value at untyped SNPs and conduct meta-analysis options
1) Impute p values for genetic association by haplotype reference data in VCF format and genotype reference data in PLINK format

java -Xmx3g -jar fapi.jar --meta --pfile ./plink.assoc1.hg19.txt,./plink.assoc2.hg19.txt,./plink.assoc3.hg19.txt --gfile 1kg.phase1.v3.asn.hg19::vcf,1kg.phase1.v3.asn.hg19::vcf, 1kg.phase1.v3.eur.hg19::vcf --p-col P,Pvalue,PValue,P --size 1000:1440,200:400,2000:400

  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
Chrom The chromosome on which a SNP is mapped.
StartPos The start position at which a SNP is mapped on a chromosome.
ID The ID of a sequence variant, it should be the rsID for most sequence variants.
Study1Type "G" denotes this SNP has inputted p value and "I" denotes this SNP has imputed p value.
Study1TConfidence 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.
Study1TP The original input or imputed p values.
Study2Type "G" denotes this SNP has input p value and "I" denotes this SNP has imputed p value.
Study2TConfidence 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.
Study2TP The original input or imputed p values.
MetaP The original input or imputed p values.
Q p-value for Cochrane's Q statistic.
I I^2 heterogeneity index (0-100).
Miao-xin Li, Professor on Precision Medical Genetics & Bioinformatics, Zhongshan School of Medicine, Sun Yat-sen University, All rights reserved.