Re: [svtoolkit-help] Input to SVAltAlign

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

Hi, Gayle,
I apologize for not responding sooner - there was something messed up in 
the mailing list so I wasn't getting these emails.
You are correct that SVAltAlign requires a sequence for the 
non-reference allele.
Genome STRiP currently doesn't have any tool to generate these, so you 
need to run tigra_sv or some other assembly tool
to generate the non-reference alleles.
This in, in part, because even if the confidence intervals are zero, we 
don't know if there is additional non-template sequence
present in the deletion allele.
-Bob

On 4/7/11 1:12 PM, svt...@li... wrote:
> Subject:
> Input to SVAltAlign
> From:
> Gayle Leen <gay...@de...>
> Date:
> Thu, 7 Apr 2011 16:52:33 +0000
>
> To:
> svt...@li...
>
>
> 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