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Old 11-25-2009, 06:31 AM   #1
Dongliang Ge
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Smile SVA: visualizing and annotating genetic variants for next-gen seq

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/


Last edited by Dongliang Ge; 03-04-2010 at 01:26 PM.
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Old 01-23-2010, 05:07 PM   #2
Dongliang Ge
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SVA is just released!

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

Last edited by Dongliang Ge; 03-01-2010 at 08:00 AM.
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Old 01-23-2010, 05:08 PM   #3
Dongliang Ge
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Its wiki page:

http://seqanswers.com/wiki/SequenceVariantAnalyzer
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Old 02-08-2010, 05:15 AM   #4
NGSfan
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Thanks! Looks interesting! I will have a try with it.
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Old 02-11-2010, 02:20 PM   #5
Dongliang Ge
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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.
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Old 02-12-2010, 08:46 AM   #6
mengmarmal
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Thanks! I will try with it for my dataset.
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Old 02-13-2010, 10:46 AM   #7
wuhoucdc
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Thanks a lot for the good package, Dongliang. I'll try it in my data.
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Old 02-20-2010, 04:54 AM   #8
Dongliang Ge
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SVA now comes on a DVD.
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Old 03-01-2010, 08:02 AM   #9
Dongliang Ge
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The website of SVA is now up:

http://www.svaproject.org/
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Old 03-04-2010, 06:41 AM   #10
roadrunner
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Hey dongliang nice seeing you here...
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Old 03-08-2010, 07:09 AM   #11
Dongliang Ge
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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

Last edited by Dongliang Ge; 03-08-2010 at 07:15 AM.
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Old 06-18-2010, 07:16 AM   #12
Dongliang Ge
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Default 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/...dromatosis.php


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Old 03-30-2011, 11:52 PM   #13
Berlinq
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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
Attached Images
File Type: jpg error2.jpg (77.0 KB, 4 views)
Attached Files
File Type: txt caco.txt (9.4 KB, 5 views)

Last edited by Berlinq; 04-05-2011 at 01:22 AM.
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Old 04-05-2011, 11:48 AM   #14
Dongliang Ge
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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


Quote:
Originally Posted by Berlinq View Post
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
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Old 05-27-2011, 12:50 AM   #15
honey
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Dongling,
Will SVA provide quantitative estimation of reads in mutated regoin? IS it mainly for SNPs or it can also detect rearrangement please?
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Old 05-27-2011, 07:54 AM   #16
Dongliang Ge
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Quote:
Originally Posted by honey View Post
Dongling,
Will SVA provide quantitative estimation of reads in mutated regoin? IS it mainly for SNPs or it can also detect rearrangement please?
Hi,

For variant or given genomic regions, yes SVA will provide summary of read depth (and other quality measures for example SNP quality).

SVA can read SNV, indel, and large SV calls, together with their quality measures. However, I need to note that SVA itself is not a variant caller. It reads variant calls (generated by for example SAMTools), and annotate and visualize them.

All the best,

Dongliang
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Old 12-06-2011, 07:49 PM   #17
iandbear
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Hi Dongliang,
Do you have any suggestion on how to detect rearrangement using whole genome sequencing data? Any tools? Thanks!



Quote:
Originally Posted by Dongliang Ge View Post
Hi,

For variant or given genomic regions, yes SVA will provide summary of read depth (and other quality measures for example SNP quality).

SVA can read SNV, indel, and large SV calls, together with their quality measures. However, I need to note that SVA itself is not a variant caller. It reads variant calls (generated by for example SAMTools), and annotate and visualize them.

All the best,

Dongliang
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