CLC bio now has support for splicing mutation analysis using the Shannon pipeline plugin. Nothing Ingenuity offers can do what this does.

This thread is WAY to informative and positive for the Rumor Mill. I suggest we bring it down a notch and make disparaging comments about Ingenuity.

I hear they eat babies in the lunchroom. I also was told that they routinely work naked and polish thier servers with pixie dust.

Too bad this forum can't emulate the informative content in this thread.

Peace out.......

Wow! Thanks for the tip on Ingenuity's technology. I just completed an alnalysis using their tool and found a possible causal variant in less than three hours. I had been struggling to find anything in my data that I could corollate to my phenotype for months. Their application pointed me to two possible causal variants and my collaborator verified in a separate data set. This software is VERY impressive.

Try ClinVar...it's new and free...and seems to be headed in the right direction.

http://www.ncbi.nlm.nih.gov/clinvar/

We are using Ingenuity's variant analysis in our lab. I'm very impressed with the software! We have used it to analyze a series of NGS derived whole exomes for a rare disease case my PI is working up. The software quickly identified a number of variants of interest our previous analysis didn't find. They have a really cool network hop functionality that uses causal reasoning to infer variant association to pathways and disease. I highly reccomend Ingenuity's product.

first choice,Ingenuity Variant analysis if you are ready to buy it. otherwise, ANNOVAR is closest. I analyzed my data with IPA and ANNOVAR, seems very close, except IPA has a great knowledge base, so providing details of variant calls,diseases, detail functions.If you are interested in biological context, then definitely go for IPA.

I have a great solution: a Postdoc!

Tried Knome software and wasn't impressed. They don't have a strong database to pull relevant biological data from. I've found very few public databass that are very good or don't require hours and hours of searching. I will give Ingenuity a try.

I just signed-up for the trial of Ingenuity variant analysis. You get two weeks free. So far pretty cool stuff. Thanks for the help!

Better to ask this over on SeqAnswers and in more detail. For my work, CLC Bio Workbench is fine, with their variant calls. But depending on the ploidy of your samples, it might not be great for your data.

Used Ingenuity variant analysis as part of their free trial a week ago. It worked really well. I din't find my next Nature paper in the data but the software helped point me in the right direction to validate a hypothesis. Give it a try. Its free now as part of a trial program. Not sure how long it runs.

ANNOVAR

Yea all we do is bitch and complain never offer any useful or constructive information. Imagine ....!

Great question. Wrong forum.