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/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/vcf2
Please advise on how to proceed, or on alternative tools. Thank you!