The following describe the process:
I choose the filter of
ICD10 includes H35.3 OR ICD10 main ICD10 H35.3
This gives 8153 out of 502410 participants.
Next at the genomics tab, gene name "CFH" was used.
This gives an allele table of 383 items.
In the exported CSV files, there is "Cohort AF" and "Cohort Allele Count",
Use cohort allele count/cohort AF I get the cohort size of 14646.
This is different from 8153 participants.
And similarly, population size is 909512, which is not the same as 502410.
Why is it so?
Can anyone let me know what is this allele count comes from? What is the field ID for this ? Is it possible that one participant has multiple measurements? How do I verify this?
Allele frequency is counted from the number of samples WES data, depending on what WES release is dispensed in the project. In your case it is probably 450K WES. You can get the number of participants by counting samples in one of the PLINK FAM files
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Allele frequency is counted from the number of samples WES data, depending on what WES release is dispensed in the project. In your case it is probably 450K WES. You can get the number of participants by counting samples in one of the PLINK FAM files
> cat "/mnt/project/Bulk/Exome sequences/Population level exome OQFE variants, PLINK format - interim 450k release/ukb23149_c22_b0_v1.fam" | wc -l
454756
Hi Anastazie, Thank you for your answer.
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