## Collected FAQs about VCF files http://gatkforums.broadinstitute.org/gatk/discussion/1318/collected-faqs-about-vcf-files
We support the Variant Call Format (VCF) for variant callsets. No other file formats are supported.
VCFTools contains a validation tool that will allow you to verify it.
No, we like VCF and we think it's important to have a good standard format. Multiplying formats just makes life hard for everyone, both developers and analysts.