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"Invalid interval" error
Occasionally I would encounter this error when combing gVCFs for the next step joint-calling/genotyping.
For example, recently I made this run:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /my/gatk/directory/gatk-package-18.104.22.168-local.jar CombineGVCFs -R /my/genome/reference/reference.fa -L 5:63300001-65300000 -O Combined.vcf -V gVCF.list
And got this:
java.lang.IllegalArgumentException: Invalid interval. Contig:5 start:63630211 end:63630210 at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:730) at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:61) at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:37) at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:49) at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:152) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$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:151) at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:113) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)
I got this error with 22.214.171.124 and recently upgraded to the current version 126.96.36.199, and the problem persisted.
There must be some variant sites in the gVCFs causing confusion for GATK, because the error only pops up for specific sites in specific windows . I have read some threads here and found some potential causes, such as overlap blocks or zero length reads. But there hasn't been a solution for this, as I have hundreds of gVCFs and it would be difficult to screen each one for such problems. Does anyone has some advices for this?