The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

# Error in VariantsToVCF

Posts: 2Member

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 • Posts: 10,408Administrator, Dev admin Hi there, Could you please try again with the latest version (2.3-9) and let us know if the error persists? Geraldine Van der Auwera, PhD • Posts: 2Member 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:

Geraldine Van der Auwera, PhD

• Posts: 2Member

Hi

Thanks.

• Posts: 2Member

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