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5.0 years ago
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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.
Hi Chris,
./plink2 --make-bed --vcf test.vcf --maf 0.05 --out test.vcf
only createstest.vcf.fam
, but not .bim and .bed files. Do I have to domake-just..
for bim and bed files?