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Structural variant analysis for single end reads

MeenuMeenu Member

HIII
I want to do structural variant analysis , have some query regarding that
1- First question is that, is this possible top do structural variant analysis of Single end reads data using Genomestrip, or is there any other software for single end reads as i found most of the tools are onl;y for paired end reads.

2- I have created sam, bam and vcf file using GATK, Still in Genomestrip main page (http://www.broadinstitute.org/gatk/guide/article?id=1534 ) 4 steps are given
SVPreprocess
SVAltAlign
SVDiscovery
SVGenotyper
Genome STRiP Functions | Components

These all steps are related to each other or i can run directly SVGenotyper as a have done all analysis using GATK.

3- How to create GenomeMask file
as i run java -Xmx2g -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.ComputeGenomeMask R CATHL4.fasta O CATHL4NEW.fasta-readLength 36 -sequence chr22, giving error
Exception in thread "main" java.lang.NoClassDefFoundError: org/broadinstitute/sv/apps/ComputeGenomeMask
Caused by: java.lang.ClassNotFoundException: org.broadinstitute.sv.apps.ComputeGenomeMask
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: org.broadinstitute.sv.apps.ComputeGenomeMask. Program will exit.

Please help me out

Thanks

Answers

  • bhandsakerbhandsaker Member, Broadie, Moderator admin
    1. You can't do Genome STRiP deletion discovery using only single-end data.
    2. If you want to run SVDiscovery or SVGenotyper, you need to run SVPreprocess first. SVAltAlign is optional and is generally not needed for longer reads (70-100bp and longer).
    3. It looks like your classpath is not set correctly (or you are using some old version of Genome STRiP). Make sure the jar files are present and located where you say they are (i.e. in the current directory) or set your classpath appropriately.
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