high missing rate for genome data converted from impute2 output

Question

[1311703846]

hey guys， I found snps will lost genotype data after my data was converted from impute2 output to vcf using plink, because the equally probability between different genotype for a snp in specific indivudual. for example : if genotype for a snp is ( 0.5,0.5,0 ) in impute2 output for a person, then genotype for this snp will be ./. after converted to vcf using plink. what can i do to solve this problem? thanks for your help!

Answer 1

[1311703846]

I found the anwser for my question :) Because there is a hard-call-threshold option in plink which control the the operation of convert.