munge_polyfun_sumstats.py
In line 62 I noticed that when the columns are renamed, freq and MAF seem to be treated the same. But couldn't these two things be different in a summary stats file? Perhaps one way would be to check if 1-freq ≤ .5, and if it is then you know it's the minor allele (and then can flip the ref/alt alleles and effect, though the specifics of this might depend on the particular file format).
munge_polyfun_sumstats.py
In line 62 I noticed that when the columns are renamed, freq and MAF seem to be treated the same. But couldn't these two things be different in a summary stats file? Perhaps one way would be to check if 1-freq ≤ .5, and if it is then you know it's the minor allele (and then can flip the ref/alt alleles and effect, though the specifics of this might depend on the particular file format).