VCF file that does not have genotyping data
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3.9 years ago
beneficii ▴ 60

So, I've got a VCF file of my whole genome sequence. I've used vcftools and plink to convert it into a bed file I merge with genotype data of people I downloaded from 1000 genomes. I then attempt to run it in admixture.

Unfortunately, admixture says that an individual lacks genotyping data, so I run plink with the --mind flag to remove them, and it turns out that individual is me! Apparently, when I converted from VCF To Plink format, there was no genotype data.

Unfortunately, I don't have access to a VCF file of my whole genome sequence that carries genotyping data specifically. Is there a way to convert my VCF file that does not have genotyping data to one that does?

vcf genotyping • 1.3k views
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