.lgen file has 3+ different alleles

Question

[Emilie]

I am trying to go from the .map .lgen .fam to a ped file so that I can convert it to a vcf file since I am more used to working with those. However when I run

plink --lfile HeartData  --recode

I get the error

Variant 'ARS-BFGL-BAC-25195' in .lgen file has 3+ different alleles.

I am using the most recent version of plink 1.9 (not 2.0 because it does not have the -lfile flag yet).

I have searched and searched and can not find a fix to this. One post suggested filtering out the one with 3+ alleles in their own file, but I could not make that work.

Any help would be appreciated!!!