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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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
The Funcotation parser doens't handle ALL_TRANSCRIPTS mode.
Variants with spanning deletions lack phase set information
ReferenceConfidenceModel using the wrong break condition in calcNIndelInformativeReads()
Treat "NaN" and "nan" as equivalents (VariantFiltration)
PairHMM related bug
ReadPosRankSumTest doesn't work for two deletions with one base in between
GenomicsDB queries overlapping deletions cause core dump
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
GATK4 VariantAnnotator does not handle PED file that GATK3 can
GenotypeGVCFs hangs in
Mutect2 and haplotypecaller require UCSC chromosome names
Inconsistent unmapped but placed query results
Create a MAFCodec for eliminating possible conflicts
SV breakpoints location off when surrounding homology are of different length, and SVLEN off when duplicated copies are of different length
Malformed VCF headers in HaplotypeCallerSpark