Variant annotator step in jointcalling procedure

[SiddhiJani]

Instructions

The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc. should be asked on the official support forum.

• Search the existing github issues to see if your issue (or something similar) has already been reported. If the issue already exists, you may comment there to inquire about the progress.
• Determine whether your issue is a bug report, a feature request, or a documentation request (for tool/class javadoc only -- for forum docs please post there)
• Consider if your "issue" is better addressed on the GATK forum: http://gatkforums.broadinstitute.org/gatk Post there if you have questions about expected tool behavior, output format, unexpected results, or generally any question that does not fit into the categories above
• Use a concise yet descriptive title
• Choose the corresponding template block below and fill it in, replacing or deleting text in italics (surrounded by _) as appropriate
• Delete the other template blocks and this header.

---

Bug Report

Affected tool(s) or class(es)

Jointcall procedure Variant Annotator step

Affected version(s)

• gatk-4.4.0.0

Description

_Describe the problem below.
13:37:19.475 INFO ProgressMeter - chr1:144419631 10967.1 2598000 236.9
13:41:49.740 INFO ProgressMeter - chr1:144447230 10971.6 2599000 236.9
13:43:46.198 INFO VariantAnnotator - Shutting down engine
[December 23, 2024 at 1:43:46 PM IST] org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator done. Elapsed time: 10,973.52 minutes.
Runtime.totalMemory()=5519704064
java.lang.IllegalArgumentException: Ref and alt alleles have same last base, hence this event is not in its minimal representation.
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:798)
at org.broadinstitute.hellbender.utils.haplotype.Event.(Event.java:31)
at org.broadinstitute.hellbender.utils.haplotype.Event.ofWithoutAttributes(Event.java:42)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.Collections$2.tryAdvance(Collections.java:4853)
at java.base/java.util.Collections$2.forEachRemaining(Collections.java:4861)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.splitVariantContextToEvents(GATKVariantContextUtils.java:1723)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator.getRsID(VariantOverlapAnnotator.java:178)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator.annotateRsID(VariantOverlapAnnotator.java:77)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator.annotateRsID(VariantOverlapAnnotator.java:63)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:370)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:334)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator.apply(VariantAnnotator.java:243)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
at org.broadinstitute.hellbender.Main.main(Main.java:306)
Using GATK jar /gpfs/data/apps/soft/gatk-4.4.0.0/gatk/build/libs/gatk-package-4.4.0.0-51-ga8b4145-SNAPSHOT-local.jar defined in environment variable GATK_LOCAL_JAR
Running:
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 /gpfs/data/apps/soft/gatk-4.4.0.0/gatk/build/libs/gatk-package-4.4.0.0-51-ga8b4145-SNAPSHOT-local.jar VariantAnnotator -R /gpfs/genetics/ngs/test_run/GRCh38_full_analysis_set_plus_decoy_hla.fa -V /gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_genotypegvcfs/TLSA_genotypegvcfs_chr1.vcf -O /gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_VA/TLSA_Variantannotator_chr1.vcf -A AlleleFraction -A BaseQuality -A ChromosomeCounts -A ClippingRankSumTest -A CountNs -A Coverage -A DepthPerAlleleBySample -A DepthPerSampleHC -A FragmentLength -A GenotypeSummaries -A LikelihoodRankSumTest -A MappingQuality -A MappingQualityRankSumTest -A MappingQualityZero -A OrientationBiasReadCounts -A OriginalAlignment -A PossibleDeNovo -A QualByDepth -A ReadPosition -A ReadPosRankSumTest -A RMSMappingQuality -A TandemRepeat -A UniqueAltReadCount --dbsnp /gpfs/data/user/siddhi/ngs/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf

Steps to reproduce

_time gatk VariantAnnotator -R /gpfs/genetics/ngs/test_run/GRCh38_full_analysis_set_plus_decoy_hla.fa -V /gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_genotypegvcfs/TLSA_genotypegvcfs_chr"+a[int]+".vcf -O /gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_VA/TLSA_Variantannotator_chr"+a[int]+".vcf -A AlleleFraction -A BaseQuality -A ChromosomeCounts -A ClippingRankSumTest -A CountNs -A Coverage -A DepthPerAlleleBySample -A DepthPerSampleHC -A FragmentLength -A GenotypeSummaries -A LikelihoodRankSumTest -A MappingQuality -A MappingQualityRankSumTest -A MappingQualityZero -A OrientationBiasReadCounts -A OriginalAlignment -A PossibleDeNovo -A QualByDepth -A ReadPosition -A ReadPosRankSumTest -A RMSMappingQuality -A TandemRepeat -A UniqueAltReadCount --dbsnp /gpfs/data/user/siddhi/ngs/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf &> /gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_VA/chr"+a[int]+"_terminal.log"

this is the command I use for all chromosme but I am geeting issue in chromosome 1.
It giving issue in chromosome 1 and it did not completed the analysis for chromosme 1.