Re: [svtoolkit-help] SV filtering steph (VariantFiltration) not working

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

No idea offhand.  Have you looked in the log file produced by queue?
What I would try is to take the log file from queue, which lists the 
java command that was run, and run this command directly.
If the behavior persists, then maybe truncate the unfiltered.vcf down to 
just the first record and if the problem still persists, then post the 
short vcf file.
-Bob

On 1/20/12 3:01 AM, Thomas Zichner wrote:
> Hi,
>
> I am running GenomeSTRiP on individual chromosomes which seems to work
> very well. In most cases, I get the file discovery.vcf as expected.
> However, in a few cases I only get discovery.unfiltered.vcf (as well as
> .discovery.unfiltered.vcf.done).
> When I rerun GenomeSTRiP, the variant filtration is executed again,
> however, there is still no output, but also no error message. And as far
> I can see, also the log file doesn't contain any error message.
>
> Any idea what the problem might be?
>
> Thank you very much!
> Kind regards
> Thomas Zichner
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help