GWAS QC step - Heterozygosity

1

Hi, I'm doing QC step with genetic data before doing imaging genetics study.

I use plink version 1.09.

I calculate heterozygosity rate to exclude individuals that has 3SD from mean value.

By calculating (N(NM)-O(HOM))/N(NM), I was able to get 'het', which is heterozygosity rate.
The result is below table.

heterozygosity calculated

I filtered 3SD away from mean value, and this sorted out 113 subjects.

But I realized that each population(White,Black,Hispanic,Asian,Others) have different distribution of heterozygosity rate clustered, and about 80 people of excluded subjects were Asian.

histogram of each population heterozygosity rate

Here are my questions.

  1. Do I have to seperate population before performing any QC?
  2. If not, do I have to just remove 80 asian, which is about half of full asian population?

Thank you.


heterozygosity


GWAS


PLINK


ImagingGenetics

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