7 days ago by
Sorry about the inappropriate error message; I'll fix that in the next build. The actual issue is that plink2 --score replaces the 'sum' modifier with direct control over the output columns. "plink2 --help score" has the following text toward the end:
The main report supports the following column sets:
maybefid: FID, if that column was in the input.
fid: Force FID column to be written even when absent in the input.
(IID are always present, and positioned here.)
maybesid: SID, if that column was in the input.
sid: Force SID column to be written even when absent in the input.
pheno1: First active phenotype.
phenos: All active phenotypes, if any.
nmissallele: Number of nonmissing alleles.
denom: Denominator of score average (equal to nmissallele value when
dosagesum: Sum of named allele dosages.
scoreavgs: Score averages.
scoresums: Score sums.
The default is maybefid,maybesid,phenos,nmissallele,dosagesum,scoreavgs.
Note the "scoresums" option at the bottom. This means that if you add "cols=+scoresums" to your --score invocation, that will add the sum column you're looking for.