2017 Oct Taeyoung Lab note

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Plink

make bed

/alima9002/program/plink-1.07-x86_64/plink --noweb --make-bed --ped variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01.ped --map variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01.map --missing-genotype N --out variant.SG.vcf.without.vege.SNP.d3.m0.2.plink.Chr01

maf

vcftools --vcf variant.SG.vcf.without.vege --maf 0.01 --out variant.SG.vcf.without.vege.maf0.01 --recode --remove-indels