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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Funcotator - Transcript position is being computed incorrectly in GencodeFuncotationFactory
HaplotypeCaller -contamination argument does not affect AD, but should
Funcotator - annotations without variant classification generated by new VariantClassification logic
# in file names converted to %23 resulting in file not found
Spark tools have problems with umlauts
GATK should preserve Picard tool exit codes
HaplotypeCaller failing when -contamination argument is supplied
Funcotator - Problems with variant alleles that span exon start/end boundaries
spark tools write bams even when .sam is specified
MannWhitneyU shouldn't do a get(double)
HaplotypeCallerSpark doesn't write g.vcf.gz files
Problem with spark.yarn.executor.memoryOverhead on DataProc
Crash with IndexFeatureFile on VCF with header but no variants
ReadsPipelineSpark: null point exception during MannWhitney permutation test
HaplotypeCallerSpark empty collection error on regions with no reads
A GATK4.0 Spark bug about HaplotypeCallerSpark and How to fix
annotate SV called with experimental tool with read and CNV call support
Tribble truncated VCF lines reading certain vcf.gzs without an index
HaplotypeCallerSpark outputs plain text instead of bgzipped VCFs when no variants present
BUILD FAILED: Javadoc generation failed
tools that expect unaligned reads shouldn't validate the sequence dictionary
Error in executing the BwaAndMarkDuplicatesPipelineSpark
Neither CollectBaseDistributionByCycleSpark nor CollectInsertSizeMetricsSpark output the PDF file
gCNV python env fails on mac
SampleDBBuilder validationStrictness argument doesn't do anything
ReferenceBases assumes that the ReferenceContext has its Window set to 10
makeGenotypeCall not called correctly in FamilyLikelihoods.java
PrintVariantsSpark crashes with serialization issues