Difference between revisions of "2017 Oct Taeyoung Lab note"
From Crop Genomics Lab.
(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