Hello everyone

I am first time working on imputation of GWAS data. I have chromosome specific VCF files. In one of the chromosome file, I have 195276 with 293 individuals. These are the steps I followed

1) Upload of VCF on Michigan imputation server with selection of reference panel All steps such as Input Validation, Quality Control and Pre-phasing and Imputation worked without any error. In report it was defined:

Excluded sites in total: 1,532 Remaining sites in total: 339,099

As output I received chr.dose.vcf.gz

2) Next, I used PLINK to get the " "bed" and "bim" file format.

./plink --vcf chr.dose.vcf.gz --make-bed --double-id --biallelic-only --out chr_biallelic

Plink log file gave me information "4057885 variants and 293 people pass filters and QC".

Its big change in no of SNPs from 195276 to 4057885. I am not sure if I am missing any intermediate information. I will appreciate all the suggestions.

Thanks in advance A