Re: [svtoolkit-help] Inquiry about Genome STRiP

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

There is post-filtering that goes on after discovery/genotyping and 
usually events that do not genotype well get filtered.
What version are you running and did you run the default QC filters?
The inbreeding coefficient filter, for example, would likely flag a site 
that is called all het (which can happen when there is too little data 
at a site to fit the mixture model).
Can you send along the complete VCF record and maybe do a plot with 
PlotGenotypingResults ?
-Bob

On 10/14/13 10:00 PM, Young-jun Kwon wrote:
> Dear, webmaster
>
> I'm a graduate student in SNU, Seoul, Korea.
>
> I used Genome STRiP for detecting CNVs, and Output vcf files were gained.
>
> Among the results, I found that there were some overlapped CNV regions 
> or some regions include other regions.
>
> Despite I considered combination of allele types, results were illogical.
>
> (real ex - all of 26 individuals have hetero(0/1) types,
> 93755407-93818770, 93755562-93818886, 93756831-93821153, 
> 93757996-93821773,.........)
>
>
> How do I have to handle this kind of result?
>
>
> Thank you.
>
> sincerely, Young-jun
>
>
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk
>
>
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help