Re: [svtoolkit-help] Regarding sample test in Genome Strip

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

First, I want to check to make sure you are using WGS data, not exome 
capture.

It would be quite unusual to see only 2 deletions on chr20 across 100 
individuals.

Are you able to share your output vcfs (e.g. one from a 100 sample run, 
one from a 50 sample run) that have discordant results?
You can email them directly to me.  Another thing to try is to genotype 
the sites (in all 100 samples is fine) and if you can share those results
and also run PlotGenotypingResults, I can take a look and see if I can 
help diagnose what's wrong.

Best,
-Bob

On 3/3/14 3:49 PM, Mishra, Pamela wrote:
>
> Hi,
>
> I am trying to find SV for 100 samples of  chromosome 20.  I already 
> ran preprocessing and discovery on these samples without any error. 
> The problem is when I look at the final vcf file, I see only 2 samples 
> being called out having SVs in the discovery phase. I checked the logs 
> and it looks like its reading and also making stats for all the 100 files.
>
> When I split the 100 samples in batches of 50 each (2 batches),one 
> batch gives me the same 2 samples that show up in the 100 sample list. 
> The  other batch gives me only 1 sample. This same sample does not 
> show any SV when its included in the 100 samples. I have done such 
> kind of tests several times but I always find the same pattern again 
> and again.  I am not sure why this is happening. I understand there 
> are a few filters listed 
> here.(http://sourceforge.net/p/svtoolkit/mailman/message/28046131/) 
>  But my idea was that the samples that show discordant pairs should 
> show up both in the list of 100 as well as when I run only 50. Could 
> you please throw your suggestion and insight into this situation. Is 
> there checks to be done?
>
> Any suggestion would be highly appreciated.
>
> Thanks,
>
> Pamela Mishra
>
>
>
> ------------------------------------------------------------------------------
> Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works.
> Faster operations. Version large binaries.  Built-in WAN optimization and the
> freedom to use Git, Perforce or both. Make the move to Perforce.
> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>
>
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help