[iandbear]

Hi Dongliang,
Do you have any suggestion on how to detect rearrangement using whole genome sequencing data? Any tools? Thanks!

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

[Dongliang Ge]

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

[honey]

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

[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

[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]

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

[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

[roadrunner]

Hey dongliang nice seeing you here...

[Dongliang Ge]

The website of SVA is now up:

http://www.svaproject.org/

[Dongliang Ge]

SVA now comes on a DVD.

[wuhoucdc]

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

[mengmarmal]

Thanks! I will try with it for my dataset.

[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.

[NGSfan]

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

[Dongliang Ge]

Its wiki page:

http://seqanswers.com/wiki/SequenceVariantAnalyzer