deleting missing genotype in a vcf file

[Eman Adel Khalil Morsi Khalil]

How to remove the variants with missing genotype more than 90% using plink2 

[ahmed fikry]

plink2 --pfile data --geno 0.9 --mind 0.1 --make-pfile --out filtered_data

Best Regards

Ahmed Fikry El-Sayed, PhD

Molecular Genetics Department

Biotechnology Research Institute

National Research Centre (NRC)
El Bohouth St,Dokki- Giza- Egypt

Postal Code : 12622
Fax: 002-02-33370931

Mob:002-01060350070

http://www.nrc.sci.eg

‫في الأربعاء، 10 سبتمبر 2025 في 4:19 م تمت كتابة ما يلي بواسطة ‪'Eman Adel Khalil Morsi Khalil' via plink2-users‬‏ <‪plink2...@googlegroups.com‬‏>:‬

How to remove the variants with missing genotype more than 90% using plink2 

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[ahmed fikry]

1-plink2 --vcf file.vcf --make-pfile --out data

2-plink2 --pfile data --geno 0.9 --make-pfile --out filtered_data

Best Regards

Ahmed Fikry El-Sayed, PhD

Molecular Genetics Department

Biotechnology Research Institute

National Research Centre (NRC)
El Bohouth St,Dokki- Giza- Egypt

Postal Code : 12622
Fax: 002-02-33370931

Mob:002-01060350070

http://www.nrc.sci.eg

‫في الأربعاء، 10 سبتمبر 2025 في 5:27 م تمت كتابة ما يلي بواسطة ‪ahmed fikry‬‏ <‪ahmedfi...@gmail.com‬‏>:‬