Forum: User Friendly VCF Filtering Tools
12
gravatar for andrew.j.skelton73
4.0 years ago by
London
andrew.j.skelton735.9k wrote:

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

ADD COMMENTlink modified 2.6 years ago • written 4.0 years ago by andrew.j.skelton735.9k

do you also put in your consideration tools that work with vcf file after annotation using other tools (ex: VEP, SnpEff, etc ...)?

ADD REPLYlink written 2.8 years ago by Medhat8.7k

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.

ADD REPLYlink written 2.6 years ago by andrew.j.skelton735.9k
2
gravatar for WouterDeCoster
4.0 years ago by
Belgium
WouterDeCoster43k wrote:

Not exactly what you are looking for but close: Genomecomb

http://genomecomb.sourceforge.net/

It doesn't work on VCF files but on tabular variant data (it has a script to convert vcf to tabular).

Disclaimer: it's produced and maintained by someone from my department

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by WouterDeCoster43k

What a nice coincidence that you are sitting near the source :) Could you be so kind and ask the maintainer (if still at the institute) if they plan to update their website with scripts to build the databases for hg38 anytime soon? Thanks in advance!

ADD REPLYlink written 2.9 years ago by ATpoint35k

if they plan to update their website with scripts to build the databases for hg38

Probably, eventually.

anytime soon

It might take a while!

(But I'll let him know)

ADD REPLYlink written 2.9 years ago by WouterDeCoster43k

Thank you I will check it out...

ADD REPLYlink written 2.8 years ago by ranjith.L0
2
gravatar for genomax
4.0 years ago by
genomax84k
United States
genomax84k wrote:

Since you appear to be including commercial tools, products from: http://goldenhelix.com/

ADD COMMENTlink written 4.0 years ago by genomax84k
2
gravatar for harold.smith.tarheel
4.0 years ago by
United States
harold.smith.tarheel4.5k wrote:

I've been happy with VCFLIB.

ADD COMMENTlink written 4.0 years ago by harold.smith.tarheel4.5k
1
gravatar for artolkamp
4.0 years ago by
artolkamp30
artolkamp30 wrote:

I'm a big fan of the easy to use vcftools which is free, very fast and has quite a bit of functionality, a big focus is on filtering variants but also does basic summary statistics such as allele frequency, fst statistics, hardy weinberg etc etc. It can also convert your vcf into different formats.

https://vcftools.github.io/man_latest.html#SYNOPSIS

ADD COMMENTlink written 4.0 years ago by artolkamp30
1
gravatar for Collin
4.0 years ago by
Collin820
United States
Collin820 wrote:

There is the CRAVAT webserver which you can upload a VCF and explore exome variants.You can download the results or use an interactive viewer for sorting/filtering/graphical display. It has several features including computationally scoring the impact of non-silent variants, population MAFs, variant quality stats, and uniprot annotations. Additionally, the interactive viewer shows the variants in protein structure. It also provides a lot of tools for analyzing somatic variants in cancer.

ADD COMMENTlink written 4.0 years ago by Collin820
1
gravatar for Pierre Lindenbaum
4.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

my colleagues work with the http://knime.org workbench. I've written some specific ngs plugins for this tool but they're quite old now: https://code.google.com/archive/p/knime4bio

ADD COMMENTlink modified 2.6 years ago • written 4.0 years ago by Pierre Lindenbaum128k
0
gravatar for steven.n.hart
2.8 years ago by
United States
steven.n.hart30 wrote:

There is also BiER app and VariantDB.

Disclaimer: I am the maintainer of VCF-Miner

ADD COMMENTlink written 2.8 years ago by steven.n.hart30

Thank you for your valuable information. I will try it out. If any issues I will let you know

ADD REPLYlink written 2.8 years ago by ranjith.L0
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