Bugs & Feature Requests
Known issues and requested enhancements

This page lists the issues tagged "bug" in the GATK4 development repository. If you have reported a bug and cannot find it in this list, let us know in the thread where you reported it. Note that we are no longer listing or processing issues in older versions of GATK (3.x and prior).

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Problem with BaseRecalibrator: java.lang.IllegalArgumentException: fromIndex(64) > toIndex(62)
Intel deflater + long reads data = intermittent corrupt bams
Funcotator reproducibly crashes on specific WES VCF record produced by GATK4.1.0 (java 1.8.0_45)
Wrong center locations in BandPassActivityProfile
CNNScoreVariants hangs when conda environment is not set up
AnalyzeCovariates produces invalid csv when readgroups contain commas, resulting in a crash
GenotypeGvcfs mangles the input phase
HaplotypeCallerSpark crashes:8 parallel GATk jobs (8 samples) using 5 Spark cpus on each in a node with 40 cpus
HaplotypeCaller emitting wrong calls when using --max-mnp-distance
Error in smith waterman native library
Funcotator returns a nullpointer exception when trying to output compressed VCF
ConcurrentModificationException in ReadsPipelineSparkIntegrationTest
Variants with spanning deletions lack phase set information
ReferenceConfidenceModel using the wrong break condition in calcNIndelInformativeReads()
Treat "NaN" and "nan" as equivalents (VariantFiltration)
ReadPosRankSumTest doesn't work for two deletions with one base in between
GenomicsDB queries overlapping deletions cause core dump
Incorrect GQ Score = 0
Bug in HaplotypeCaller: lack of consistency in the overlap criteria applied to reads to be considered for PL and AD/DP annotations.
README: R setup for running tests may need OS X update
GermlineCNVCaller: Odd behavior of the log dumped ELBO values vs the real tracked ELBO values in tracker-tar
Funcotator does not always annotate multiallelic VCF records with both an insertion and deletion correctly
GATK v4.0.8.1 GenomicsDBImport Error (VariantStorageManagerException exception); File syncing error
Got "Too many open files" when use BaseRecalibratorSpark
AddCommentsToBam function does not handle colon in the -C flag
CRAMs generated by GATK don't always have M5/UR attributes in the sequence dictionary
HaplotypeCaller should use realigned reads for ref conf calc in flanking regions
Make CombineGVCFs and GenomicsDBImport properly compute AD over overlapping deletions