Convert VCF to pg_snp and gd_snp

When using “VCF to pg_snp” (with idea to reformat later to gd_snp), Galaxy fails. The tool does not accept that some alleles have alternatives:

An error occurred with this dataset:
format interval database ?
bad variant nt AAGA,AATG for nt 2 at /cvmfs/

Please advise on how to proceed, or on alternative tools. Thank you!