Convert the mimimac2 imputation probability vcf file into plink (ped, map) format

When I do the imputation using mimimac2, the results showed like below:

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    1_201312170-01    2_201312504-01    6_201313899-01
1    882803    1:882803    A    G    .    PASS    MAF=0.07281;R2=0.80674    GT:DS    1|1:1.990    1|1:1.970    1|0:1.043

I tried to convert into plink (ped, map) file using the plink1.9

plink1.9 --vcf file --recode --out data

It did work, but I am not sure whether it is correct or not? As I am not quite sure what does the probability format: 1|1:1.990 means? Could anyone explain to me?

snp genome

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updated 4.5 years ago by Ram

• written 11.7 years ago by aydzhouyuan •

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