Re: [svtoolkit-help] PlotGenotyping and tigra_sv

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

On 9/14/12 8:36 AM, Ankita igib wrote:
> Hi Bob,
>
> I have few more issues, i am trying to use plotgenotyping module using 
> command as follows
> command -
> java -cp 
> /data1/home/ankita/1000G_Data/svtoolkit/lib/SVToolkit.jar:/data1/home/1000G_Data/svtoolkit/lib/gatk/GenomeAnalysisTK.jar 
>  org.broadinstitute.sv.apps.PlotGenotypingResults  -site DEL_147 -o 
> test.pdf -rundirectory .
>
> Error - Exception in thread "main" java.lang.NoClassDefFoundError: 
> org/broadinstitute/sv/apps/PlotGenotypingResults
> Caused by: java.lang.ClassNotFoundException: 
> org.broadinstitute.sv.apps.PlotGenotypingResults
> at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:319)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:264)
> at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:332)
>
> I tried to find, but couldn't find the answer.
This is newer functionality only available in more recent interim releases.
If you want to use this, you should download the latest interim release.
>
> (ii) for tigra_sv installation - i got cmake file, main.cpp samtools.h 
> file for installation but unable to install it, Can you guide ?
No, you'll have to contact someone at WashU.
>
> (iii) While using alt_alignment, we have to  provide unmapped bam 
> files separately or tool can identify the flags for unmapped reads in 
> a bam file (supposed downloaded from 1000 Genomes), how to use 
> tigra_sv in alt_alignment steps, as output of tigra_sv is a text file 
> of breakpoints.
If you have sequencing data with longer paired reads (75-100bp) there is 
very little value in using completely unmapped read pairs and the alt 
alignment steps.
It is more important if you have short 36 bp reads or unpaired data.
Unmapped mates (stored in your bam files at the same POS as the mapped 
mate) will be used for split-read genotyping by default.

I don't have a tool to convert the tigra_sv output into a well-formed 
vcf, which is what you will need to do to use breakpoints in genotyping.

-Bob
>
> -- 
> ------------
> Regards
> Ankita
> DST Inspire Fellow (Graduate Student)
> Lab no 604A
> G.N. Ramachandran Knowledge Center for Genome Informatics
> Institute of Genomics and Integrative Biology (CSIR)
> North Campus DU, Near Jubliee Hall
> Delhi - 110007
>
>
> http://igvbrowser.igib.res.in
>
>
>
>
>
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