Association of allele in population
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7 weeks ago
Nai ▴ 20

I have vcf file which belongs to cases only. I have to calculate frequencies and pvalue and odds ratio. It showed note: NO phenotypes present. I used flags --allow-no-sex --no-FID

Kindly help me to get-rid off.

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You can't calculate p-value or odds ratio if you only have cases (assuming you are analysing a binary case control trait?)

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No...I have GWAS vcf file only with genotype information

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OK well if you only have cases then you cannot calculate an pvalue. Is this for a school project or something?

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Thank you. Its dissertation project. I have only GWAS with cases

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