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Plink --freq case-control output format

I used plink to generate MAF statistics but I am not sure about the output format.

The command I used is "plink --bfile <my file=""> --freq case-control --out temp --1".

In the output file "temp.frq.cc", the column names are "CHR, SNP, A1, A2, MAF_A, MAF_U, NCHROBS_A, NCHROBS_U". I am not sure which one is case and which one is control (MAF_A and MAF_U).

Could anyone give some suggestions, please? Thank you very much.

plink snp
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updated by Maxime Lamontagne Maxime Lamontagne • written by gaosong0329 • gaosong0329

1 answer

https://www.cog-genomics.org/plink2/formats#frq_cc

CHR Chromosome code

SNP Variant identifier

A1 Allele 1 (usually minor)

A2 Allele 2 (usually major)

MAF_A Allele 1 frequency in cases (Affected)

MAF_U Allele 1 frequency in controls (Unaffected)

NCHROBS_A Number of case allele observations

NCHROBS_U Number of control allele observations

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written by Maxime Lamontagne Maxime Lamontagne

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