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Error in VariantsToVCF

Member

Hi

I am trying to covert the UCSC format of SNP to VCF format. I downloaded dbSNP128.txt.gz from (UCSC http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/snp128.txt.gz). The command I used is
java -jar GenomeAnalysisTK.jar -R mm9.fa -T VariantsToVCF --variant:OLDDBSNP dbSNP128.txt -o dbsnp128.vcf`

Error message:

ERROR stack trace

java.lang.IllegalArgumentException: Duplicate allele added to VariantContext: G
at org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors$DBSnpAdaptor.convert(VariantContextAdaptors.java:206) at org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors.toVariantContext(VariantContextAdaptors.java:64) at org.broadinstitute.sting.gatk.walkers.variantutils.VariantsToVCF.getVariantContexts(VariantsToVCF.java:177) at org.broadinstitute.sting.gatk.walkers.variantutils.VariantsToVCF.map(VariantsToVCF.java:123) at org.broadinstitute.sting.gatk.walkers.variantutils.VariantsToVCF.map(VariantsToVCF.java:83) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:120) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:67) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:94) ERROR ------------------------------------------------------------------------------------------ ERROR A GATK RUNTIME ERROR has occurred (version 2.3-4-g57ea19f): 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: Duplicate allele added to VariantContext: G ERROR ------------------------------------------------------------------------------------------ According to this post (http://gatkforums.broadinstitute.org/discussion/1275/error-in-haplotype-caller), "Duplicate allele added to VariantContext" error may be caused by lower case bases in the reference. I converted all my reference sequences to upper case letters, but GATK still reports the same error message. Thanks in advance. Tagged: Best Answer Answers • Cambridge, MAMember, Administrator, Broadie Hi there, Could you please try again with the latest version (2.3-9) and let us know if the error persists? • Member Hi, I tried the latest 2.3-9. Still the same error. ERROR ------------------------------------------------------------------------------------------ ERROR stack trace java.lang.IllegalArgumentException: Duplicate allele added to VariantContext: G at org.broadinstitute.sting.utils.variantcontext.VariantContext.makeAlleles(VariantContext.java:1307) at org.broadinstitute.sting.utils.variantcontext.VariantContext.(VariantContext.java:290) at org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:495) at org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors$DBSnpAdaptor.convert(VariantContextAdaptors.java:206)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231)

ERROR ------------------------------------------------------------------------------------------

OK, thanks for trying. We'll need you to narrow down the error to the offending record and upload a snippet to our FTP server so that we can reproduce the error and fix the bug. Please see this article on how to do that:

• Member

Hi

Thanks.

• Member

I need to run the exact same command with dbSNP 132 for mm9. Has this fix been implemented in 2.3-9? If it isn't available til 2.4 then when will that be released?

-Phil