Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Collected FAQs about VCF files

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,235Administrator, GSA Member admin
edited October 2012 in FAQs

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.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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