Does anyone know any ANNOVAR alternatives for Whole Genome Sequencing with flexible filters for annotations of a VCF file?

Question

[screadore]

Hello everyone,

I'm looking to find alternatives to ANNOVAR whole genome sequencing annotations that offers flexible filtering options for non-coding regions of DNA? If anyone has any experience of open source tools used for this please let me know. Thank you.

[berick]

I add myself here. What's wrong with Annovar is that no direct download is possible. Which is enough to look for alternative: neither Conda or Docker containers, no way to include it in a Docker container if you want to redistribute it.

[karl.stamm]

What's wrong with ANNOVAR that you want different?

Answer 1

[berick]

As an update, we didn't find a compatible alternative so we and our collaborators decided to completely abandon ANNOVAR and use VEP which is much easier to install, update and maintain and can be legally deployed without being forced to ask for a download link.