Difference between revisions of "2017 Oct Taeyoung Lab note"

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(Created page with " ==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.wit...")
 
 
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===make bed===
 
===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
 
  /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

Latest revision as of 05:07, 31 October 2017

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