1. What file formats do you support for variant callsets?
We support the Variant Call Format (VCF) for variant callsets. No other file formats are supported.
2. How can I know if my VCF file is valid?
VCFTools contains a validation tool that will allow you to verify it.
3. Are you planning to include any converters from different formats or allow different input formats than VCF?
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.