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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MAFOutputRenderer produces an empty file when the input VCF has no variants to render.
Transcript list (userRequestedTranscripts) is acting as a filter, when it should be for prioritizing transcripts during selection.
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
The combination of ReadsDownsamplingIterator + ReservoirDownsampler does not work correctly
GenomicsDB errors discovered in the wild
Picard version doesn't print correctly when running a Picard tool from GATK
GenomicsDB Import/Select fails on record containing a spanning deletion allele
java.lang.IllegalArgumentException: Invalid interval.
barclay fails to set collection arguments initialized with an immutable collection
This variant definitely shouldn't pass M2 filtering
Please fix the broken 3.8-1 release with wrong pom.xml
Users reporting unreasonable memory usage in GenotypeGVCFs
`__pthread_tpp_change_priority` error in GenotypeGVCFs (GATK 4.0.0.0)
GATK4 GenomicsDB error with GenomicsDB versions 0.9.0 and 0.9.2
gatk sets TMP_DIR globally readable/writable for any user
GenotypeGVCFs takes a long time on small interval
funcotator and file locking
Funcotator - Fix INDEL start/stop position and alleles for ALL output types
# in file names converted to %23 resulting in file not found
Spark tools have problems with umlauts
Funcotator - Problems with variant alleles that span exon start/end boundaries
MannWhitneyU shouldn't do a get(double)
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