HaplotypeCaller 2.4
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Comments (16)

I am getting the following error. What is the minimum read size to do assembly? 50 basepair too short?

ERROR stack trace

java.lang.IllegalStateException: Reads are too small for use in assembly. at org.broadinstitute.sting.gatk.walkers.haplotypecaller.DeBruijnAssembler.createDeBruijnGraphs(DeBruijnAssembler.java:139) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.DeBruijnAssembler.runLocalAssembly(DeBruijnAssembler.java:123) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:483) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:132) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:552) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:512) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:244) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.ja at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.j at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283 at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:1 at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:24 at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:15 at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ---------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-3-g2a7af43):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Reads are too small for use in assembly.
ERROR ---------------------------------------------------------------------------------------

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