Tagged with #read-backed phasing
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Hello,

I am trying to use Read-backed Phasing for merging cis variants in my vcf file. The vcf was generated using GATK. I am encountering the following error:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Badly formed variant context at location chr1:205640992; no padded reference base was provided. at org.broadinstitute.sting.utils.variantcontext.VariantContext.validateReferencePadding(VariantContext.java:1246) at org.broadinstitute.sting.utils.variantcontext.VariantContext.validate(VariantContext.java:1226) at org.broadinstitute.sting.utils.variantcontext.VariantContext.validate(VariantContext.java:1221) at org.broadinstitute.sting.utils.variantcontext.VariantContext.(VariantContext.java:374) at org.broadinstitute.sting.utils.variantcontext.VariantContext.(VariantContext.java:243) at org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.reallyMergeIntoMNP(VariantContextUtils.java:1061) at org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.mergeIntoMNP(VariantContextUtils.java:1009) at org.broadinstitute.sting.gatk.walkers.phasing.MergeSegregatingAlternateAllelesVCFWriter.add(MergeSegregatingAlternateAllelesVCFWriter.java:182) at org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriterBase.emitRecords(SortingVCFWriterBase.java:135) at org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriterBase.emitSafeRecords(SortingVCFWriterBase.java:95) at org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriterBase.add(SortingVCFWriterBase.java:125) at org.broadinstitute.sting.gatk.walkers.phasing.WriteVCF.writeVCF(WriteVCF.java:32) at org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker.writeVCF(ReadBackedPhasingWalker.java:1060) at org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker.writeVcList(ReadBackedPhasingWalker.java:1054) at org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker.reduce(ReadBackedPhasingWalker.java:1016) at org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker.reduce(ReadBackedPhasingWalker.java:89) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:79) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:149) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.2):
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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Badly formed variant context at location chr1:205640992; no padded reference base was provided.

The corresponding vcf entry is : chr1 205640992 . T TCAAA 43296.89 PASS AC=2;AF=1.00;AN=2;DP=668;FS=0.000;HRun=0;HaplotypeScore=5455.5058;MQ=69.88;MQ0=0;QD=64.82 GT:AD:DP:GQ:PL 1/1:172,495:668:99:43297,1755,0

Could you please help if am missing something here.