GATK4 MergeVcfs / ValidateVariants does not support ambiguous (IUPAC) variants (b37 reference)
Perhaps this is intended, but GATK4 MergeVcfs / ValidateVariants do not support variants with ambiguous annotation, ie.
3:60830534-60830534 (M) in b37.
ValidateVariants returns the following error when trying to validate a VCF file with such a base:
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number n: unparsable vcf record with allele M