Should I assume that the genotype of the 1000 Genomes project individuals in positions that are not in the vcf file, are homozygous for the reference allele?
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5.2 years ago
magda ▴ 20

I want to merge my variant data with those from the 1000 genomes project, but which genotype can I assume that the 1000 Genomes project individuals have in the positions that are not included in their vcf files. Should I assume that they are homozygous for the reference allele? But what if in that position an individual don't have any reads? Do you know if they provide a g.vcf file, with information in all positions (reads, etc..., which I haven't found. Is there a way of extracting the genotype without having to apply the whole pipeline in the Bam files they provide? What do you do?

Thank you Magda

reference allele 1000 genomes project vcf • 1.0k views

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