How to filter and impute missing snps in vcf file

Question

[Kumar]

Hi Guys, I have a merged vcf file of 90 individuals vcf files. I am looking to use the file for my population structure analysis at fastStructure.

I found that there are several junk and missing SNPs in the file. I used TASSEL to impute the missing SNPs but it did not work at fastStructure analysis. I tried --proxy-impute all and --geno 0 options at plink. However, I could not figure out the appropriate solution.

Please suggest any method for filtering and imputation the missing SNPs in vcf file.

Thank you!