Hi,
I'm attempting to gather together resources for user friendly ways to filter / interrogate VCF/ variant data. Variant Calling produces a lot of data, particularly for larger studies, and becomes quite difficult to present results to end users. I thought it'd be useful to document any resources that would be useful in presenting this kind of data.
From my Google-Fu, I've found the following resources:
Gemini - A fantastic SQLite based tool to analyse trios, complex pedigrees and singletons for possible disease causing variants. There's currently Bulletin (Gemini's internal browser interface), which is under development, and Puzzle, which is also under active development (integrates well with Gemini databases and VCF files).
Ingenuity Variant Analysis - QIAGEN (Skynet) - Quick filtering, (relatively) friendly interface, however comes with a pretty hefty price tag, and the fact that you're sending all your valuable data to a mysterious black box ("knowledge Base")
VCF-MINER - From the Mayo Clinic - Just in the process of getting this running, but I'll edit with my experiences.
If I've missed any major tools, please add them in as an answer below.
Update Nov 2017:
I ended up using Seqr (Macarthur Lab) for the project I was working on. It's a bit of a pain to set up locally, but the devs are still highly active in developing it, currently they seem to be engineering annotation with Hail. It's designed around rare variants and integrates the Gemini methods of inheritance filtering. Excellent piece of software.
Also out relatively recently is MendalMD
do you also put in your consideration tools that work with vcf file after annotation using other tools (ex: VEP, SnpEff, etc ...)?
I'd consider annotation tools to be a separate issue, while tools such as VEP can produce tab delimited output, the crux of this post is then how to present / filter these annotations in a user friendly way.