i use shapeit to do phasing and then inpute2 to generate the gen file.
but after i performing association test to the gen file and finally get a assoc.dosage file, i found that the p-value of original snp (not the imputed snp) is different from the original one (before phasing and impute).
my original plink file is hg19.
here is my comment line:
./shapeit --input_bed mygwas.chr1.bed mygwas.chr1.bim mygwas.chr1.fam \
--input-map genetic_map_chr1_combined_b37.txt \
--output-max mygwas.phased.haps mygwas.phased.sample
./impute2 -use_prephased_g \
-m genetic_map_chr_combined_b37.txt \
-h ALL_1000G_phase1integrated_v3_chr1_impute.hap \
-l ALL_1000G_phase1integrated_v3_chr1_impute.legend \
-known_haps_g mygwas.phased.haps \
int xxx xxx \
Ne xxx \
-o mygwas.gen \
./plink --dosage mygwas.gen format=3 dose=1 skip0=1 skip1=1 noheader --fam mygwas.fam --assoc --out mygwas.imputed.
i think the p-value of original SNP in the mygwas.chr1.bed/bim/fam file should be the same with the output mygwas.imputed.assoc.dosage, but the result showed that they are different. and this really confused me.
could everyone tell me how should i fix this problem? really thanks a lot