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

Links of MX Li's tools:

Impute association p-values at untyped SNPs options

1) Impute p values for genetic association by haplotype reference data in VCF and Plink binary format

java -Xmx3g -jar fapi.jar --impute --pfile ./assoc1.hg19.txt,./plink.assoc2.hg19.txt --gfile 1kg.phase1.v3.asn.hg19::vcf,abc::plink --out result1,result2

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.
Type "G" denotes this SNP has inputted p value and "I" denotes this SNP has 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.
P The original input or imputed p values.

Miao-xin Li, Professor on Precision Medical Genetics & Bioinformatics, Zhongshan School of Medicine, Sun Yat-sen University, All rights reserved.