Re: [svtoolkit-help] Input to SVAltAlign

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

Hi, Gayle,

Also, if you haven't looked at it, there is a presentation here:
http://www.broadinstitute.org/gsa/wiki/index.php/Main_Page#GSA_Feb._17th_2011_next-generation_sequencing_workshop

On slide 5, I tried to give a roadmap for a "soup to nuts" pipeline 
along the lines of what we used for the 1000 Genomes pilot.

-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
>
>
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