It's been a while since I last used Plink to calculate IBS/IBD. For a given VCF file,
test.vcf, I did maf filtering and calculated IBD with these commands:
plink --vcf test.vcf --maf 0.05 --recode --out test.vcf plink --file test.vcf --genome
Do I also need to do Hardy-Weinberg or any other filtering before these steps? Could someone please clarify.