Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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