--altMAF required to get correct allele frequency

[welchr]

We need to include the —altMAF flag to get allele frequencies calculated on only files contributing the variant (i.e., not assuming MAC=0 for studies without the variant in the file). This is quite different than one would expect for default operation.

[welchr]

This seems to be intentional behavior on the part of the original authors. From the wiki:

In a single study of sample size N, if a site is monomorphic or not reported in vcf/ped, it is considered that the sample size of this study is not large enough to sample the rare allele. Thus, this study contributes 2*N reference alleles and 0 alternative allele towards meta-analysis. To let such studies contribute no alleles towards pooled allele frequency, specify --altMAF.

I think changing how this works now would end up making a backward incompatible change to the program, so this maybe would be better for a future 5.0.0 release.