Re: [svtoolkit-help] Input to SVAltAlign

[Bob H. <han...@br...>]

Hi, Gayle,
You are correct: the problem is that SVAltAlign requires base-pair-exact 
breakpoints and SVDiscovery does not currently produce these.
If you want to genotype using breakpoints, you need to run tigra_sv or 
some other tool (I think at Sanger they are using velvet).
Note that a confidence interval of zero is not exactly the same as 
knowing the alt allele at base pair resolution.
The confidence interval is actually based on the confidence in the 
difference in length between the ref and alt alleles.
This is different than the number of deleted bases from the reference if 
the alt allele contains non-template sequence.
-Bob

On 4/7/11 12:52 PM, Gayle Leen wrote:
> Hi,
>
> I'm trying to run Genome STRIP on a dataset but the output from the 
> SVDiscovery module (the vcf file) can't be used as input to 
> SVAltAlign. I think this is because the potential variants are tagged 
> as 'imprecise', even though the confidence intervals around the ends 
> are 0 for some events - consequently the alternative allele sequence 
> isn't generated. Is there some way of getting around this? Or should I 
> use some other algorithm such as tigra_sv to process the vcf file?
>
> If you could help me with this that would be great,
>
> Gayle
>
>
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
>
>
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help