SequenceVariantAnalyzer: analyzing genetic variants from next-gen sequencing

[Dongliang Ge]

Friends,

If you are working on next-generation sequencing studies, particularly if you are interested in annotating, visualizing SNPs, INDELs, CNVs, and identifying genetic variants responsible for biological traits or diseases, please check out our software tool SequenceVariantAnalyzer (SVA):

http://www.svaproject.org/

SVA is designed for two specific aims:

1. To annotate the biological functions of the identified genetic variants, organize and visualize them;
2. To help find the genetic variants that are associated with or responsible for the biological traits or medical outcomes of interest.

The SVA release package comes with an example project extracted from 10 genomes - 5 cases and 5 controls. To reduce the size of the release package, I release only the data on chromosome X. The web page below shows that you can play with SVA and an example project to "identify (again )" the Factor VIII (F8) gene for type A hemophilia:

http://www.svaproject.org/fastrun.php

SVA is also featured with an integrated genome browser to help an investigator to explore the user-generated data and data from public domains. Here is a screenshot:

http://www.svaproject.org/screenshot1.php

Particularly, SVA genome browser allows you to conveniently 'introduce' key variants that you identified to compare and see the difference they could make.

Please give it a try and let us know what you think.

Lastly, I hope you may find this tool helpful for your next-generation discovery!

Best regards,

Dongliang Ge,
Duke University, USA
http://people.genome.duke.edu/~dg48/

[Dongliang Ge]

SVA is just released!

Check it out at: http://www.svaproject.org/

[Dongliang Ge]

Its wiki page:

http://seqanswers.com/wiki/SequenceVariantAnalyzer

[NGSfan]

Thanks! Looks interesting! I will have a try with it.

[Dongliang Ge]

SVA comes with two editions:
1. Standard edition : ~2.2 Gb. This edition has full annotation functions.
2. Lite Evaluation edition: ~ 250Mb. This edition does not have annotation function, but can be used to load an example project for evaluation purposes.

Both editions are free for use.

[mengmarmal]

Thanks! I will try with it for my dataset.

[wuhoucdc]

Thanks a lot for the good package, Dongliang. I'll try it in my data.

[Dongliang Ge]

SVA now comes on a DVD.

[Dongliang Ge]

The website of SVA is now up:

http://www.svaproject.org/

[roadrunner]

Hey dongliang nice seeing you here...

[Dongliang Ge]

Friends,

A lite evaluation edition is released for Windows. Play with it on your laptop!

http://www.svaproject.org/download.php#win

I would also take this chance to thank all the users and their comments!

Here I have a screenshot on a Dell E6400 laptop with 32-bit Windows XP:




Larger version:

http://www.svaproject.org/images/sva_win32.png

[Dongliang Ge]

Causal variants for metachondromatosis are identified.

Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

Sobreira NLM, Cirulli ET, Avramopoulos D, Wohler E, Oswald GL, et al. (2010) PLoS Genet 6(6): e1000991. doi:10.1371/journal.pgen.1000991

http://people.genome.duke.edu/~dg48/sva/metachondromatosis.php

[Berlinq]

Dear Dongliang
Trying, still not working. My input files (SNV and INDEL) look ok, as described in the manual, get an error - please see attachments (also gsap file as a txt)
Second problem is that after updating to version 1.02 the programm is asking for CNV tagging data file, Venter's SNP and INDEL files wich are missing in the package.. Where do I get it from?
kind regards

[Dongliang Ge]

Hi Berlinq,

Thanks for the message.

In your .gsap script file, please change the indel file name extension to .samtoolsindels. That is,

[INDELINPUT]=cacoind,/project/erasys1/ngs/sva/svacaco/caindel.samtoolsindels

In addition, there is a new SVA version version 1.1 available now. In the new version, the newer vcf format, instead of the older samtools pileup format (the .samtools and .samtoolsindels files), are supported.

Best,
Dongliang

Dear Dongliang
Trying, still not working. My input files (SNV and INDEL) look ok, as described in the manual, get an error - please see attachments (also gsap file as a txt)
Second problem is that after updating to version 1.02 the programm is asking for CNV tagging data file, Venter's SNP and INDEL files wich are missing in the package.. Where do I get it from?
kind regards

[honey]

Dongling,
Will SVA provide quantitative estimation of reads in mutated regoin? IS it mainly for SNPs or it can also detect rearrangement please?