HaplotypeCallerSpark - "Caused by: java.lang.IllegalArgumentException: Sequence ... filters= added out of order currentReferenceIndex: 9, referenceIndex:11" Error

[gokalpcelik]

Hi
This is an issue derived from the GATK forum.

https://gatk.broadinstitute.org/hc/en-us/community/posts/17996976455067-HaplotypecallerSpark-error?page=1#community_comment_18161302676123

User is having an issue with HaplotypeCallerSpark possibly a traversal issue. This problem was also present in the past in another github issue

#7199

User tried with the latest version as well and even providing a bed file as in the former issue did not help solve the problem. HaplotypeCaller works fine with or without the bed file but Spark version does not.

Here is the error message

**Caused by: java.lang.IllegalArgumentException: Sequence [VC HC_call @ NW_020555792.1:138 Q78.32 of type=SNP alleles=[T*, G] attr={AC=2, AF=1.0, AN=2, DP=2, ExcessHet=0.0000, FS=0.000, MLEAC=[1], MLEAF=[0.5], MQ=47.00, QD=29.09, SOR=0.693} GT=[[AR0111 G/G GQ 6 DP 2 AD 0,2 PL 90,6,0]] filters= added out of order currentReferenceIndex: 9, referenceIndex:11
        at htsjdk.tribble.index.tabix.AllRefsTabixIndexCreator.addFeature(AllRefsTabixIndexCreator.java:79)
        at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.add(IndexingVariantContextWriter.java:203)
        at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:242)
        at org.disq_bio.disq.impl.formats.vcf.HeaderlessVcfOutputFormat$VcfRecordWriter.write(HeaderlessVcfOutputFormat.java:93)
        at org.disq_bio.disq.impl.formats.vcf.HeaderlessVcfOutputFormat$VcfRecordWriter.write(HeaderlessVcfOutputFormat.java:56)
        at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.write(SparkHadoopWriter.scala:368)
        at org.apache.spark.internal.io.SparkHadoopWriter$.$anonfun$executeTask$1(SparkHadoopWriter.scala:138)
        at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1538)
        at org.apache.spark.internal.io.SparkHadoopWriter$.executeTask(SparkHadoopWriter.scala:135)
        ... 9 more
01:50:24.007 INFO  ShutdownHookManager - Shutdown hook called**

User was informed that this is a bug and needs fixing therefore sticking with HaplotypeCaller is the best solution.