--mac vs --maf on dosage

[Yang Li]

Hi Chris,

I'm using Plink2 for GWAS and wondering:

1. will --mac be redundant with --maf on large sample size  when mac_threshold <= maf_threhold*sample_size ?

2. will --mac use any dosage information? If not, does --mac count for the alleles with least count for multi-allelic sites?

Thanks,

Yang

[Chris Chang]

1. Yes, if there are no missing dosages, --mac is redundant with --maf in that scenario.  Note that missing dosages don't count toward sample size.

2a. Yes, plink2 --mac uses dosages when they are available.  The online documentation has been clarified accordingly.

2b. Concerning multiallelic variants, from the online documentation:
By default, these flags operate on 'nonmajor' (i.e. sum of all but the largest value) allele frequencies/dosages. Three other modes are supported: 'nref' (nonreference), 'alt1', and 'minor' (smallest). You can use bcftools-style freq:mode notation for this.

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