Changing/swapping per-sample calls

[Matthew Maher]

I have a dataset I was supplied it which it's been determined that somewhere upstream there was some allele confusion and thus for a small set of variants (these are all bi-allelic), I want to change the actual per-sample calls - e.g. if it's a A/C variant, I want any AAs to become CCs and vice versa. 

Is there a PLINK* option to do this? 

I do not want --flip as that's for strand problems; i.e. the current two alleles are correct
I do not want to change what's REF and whats ALT
i.e. I think my pvar is just fine, and this should be a change within the pgen.

Thanks for any info and thanks for PLINK*

[Chris Chang]

One way to do this with PLINK 1.9 is to create small fileset(s) with just the genotypes you want to patch in, and then use --merge-mode 3 (putting the newly-created fileset(s) last in the merge order).

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