个体中0/0基因型是否应该被去除

JW
Junhao Wang
Oct 10, 2023
protocol Protocol: Genomic Genetic Load Analysis

老师,您好,对于“将每个注释结果划分为纯合(0/0或者1/1)和杂合(0/1)”这一步,您前面的步骤已经将个体vcf提取出来了,个体中0/0等位基因表示未发生突变,是不是应该继续将个体vcf中的0/0基因型去除掉,再进行后续的步骤分析?

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Junhao Wang Answered Oct 14, 2023

Ocean university of China

Thank you for your response, Professor Yu! I understand now. Additionally, in the analysis of differences in the Loss of Function (LOF) genetic burden, if a small subset of individuals in the population (such as 5 individuals) has a LOF site count of 0, should these 5 individuals be treated as missing data, or should they be included in the analysis?

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黎 于 Author Answered Oct 13, 2023

This depends on your outgroup, if your allele in outgroup is 1/1, then 0/0 is the derived allele, so you still have to keep it. If you don't have a suitable outgroup, you can only define the ancestral alleles in terms of relatively high frequency alleles.

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