I have a large SNP data, I'm trying to remove the SNPs with minor allele frequency (MAF) < 5% and the ones that don't follow Hardy-weinberg equilibrium . I'm using R and I don't know which package does that
any help please
If you don't use GATK, then programs like vcfTools and bcfTools could probably help, otherwise you have you write your own Perl/Bash/Python/whatever scripts. Plink 1.9 is good too https://www.cog-genomics.org/plink2. You have to convert your vcf into just plink format genotypes, then it's easy to filter by MAF, and HWE.