combine gvcf error

Question

[GK1610]

I am trying to combine 240 gvcf files to run joint GenotypeGVCFs. I created 12 meta-merged-GVCFs by combining 20 samples into one.and I did this separately for each chromosome. When I combine 12 metamerge files for each chromosome, i get this error

09:54:21.509 INFO CombineGVCFs - Shutting down engine
[March 27, 2018 9:54:21 AM EDT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 1.10 minutes.
Runtime.totalMemory()=6771179520
java.lang.IllegalArgumentException: Unexpected base in allele bases '*AAAAAAAAC'
at htsjdk.variant.variantcontext.Allele.(Allele.java:165)
at htsjdk.variant.variantcontext.Allele.create(Allele.java:239)
at org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.extendAllele(ReferenceConfidenceVariantContextMerger.java:406)
at org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.remapAlleles(ReferenceConfidenceVariantContextMerger.java:178)
at org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:70)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.endPreviousStates(CombineGVCFs.java:340)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.createIntermediateVariants(CombineGVCFs.java:189)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.apply(CombineGVCFs.java:134)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:73)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:110)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:108)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:118)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
at org.broadinstitute.hellbender.Main.main(Main.java:277)

Answer 1

[Pierre Lindenbaum]

looks like a bug. The same issue has been posted on github https://github.com/broadinstitute/gatk/issues/4525

CombineGVCFs java.lang.IllegalArgumentException: Unexpected base in allele bases '*AACC'

[GK1610]

Do you have any suggestion to remove this?

[Pierre Lindenbaum]

sed 's/\*AACC/AACC/' f1.gvcf > f2.gvcf

[GK1610]

sed 's/*ATCAAATG/ATCAAATG/' temp1.gvcf > temp1.flt.gvcf sed 's/*ATCAAATG/ATCAAATG/' temp2.gvcf > temp1.flt.gvcf

java -jar $GenomeAnalysisTK_jar CombineGVCFs -R $REF -V temp1.gvcf -V temp2.gvcf -O merged.gvcf I am still getting this error :(

java.lang.IllegalArgumentException: Unexpected base in allele bases '*ATCAAATG'