Regenie requires FID to be present in .psam files although it is optional in the spec

[pettyalex]

This is very similar to #105, although that issue looked like it focused on pgen parsing problem.

The pgen release of All of Us data is compliant with the spec with a header of #IID SEX, but Regenie refuses to process it, saying psam : [exome.chr22.psam] ERROR: invalid header (must start with #FID [not #IID]).

The specification says "(FID must either be the first column, or absent. If it's absent, all FID values are now assumed to be '0'.)": https://www.cog-genomics.org/plink/2.0/formats#psam

I observed this on the v4.1.gz release.

[joellembatchou]

Hi Alex,

REGENIE does not currently support this format but it can be added in future releases. Is FID also 0 in the phenotype/covariate files you are including?

For now, one workaround would be to add in a #FID column & write that to a new PSAM file then symlink the PVAR/PGEN file with the same prefix as the new PSAM file.

Cheers,
Joelle