Bugs & Feature Requests
Known issues and work in progress

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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ReadGroupBlackListReadFilter doesn't filter reads when used from the command line
SelectVariants hangs while selecting INDEL type
java.lang.IllegalArgumentException: Unexpected base in allele bases
SelectVariant raise OutOfMemoryError
BQSR can produce tables with missing ReadGroups
Mutect2 fails when secondary alignments in same assembly region as primary
GT and PGT fields have discorant genotypes for 7% of the variants
NullPointerException error while running VariantEval
IllegalArgumentException: beta must be greater than 0 in FilterMutectCalls
Funcotator shuts down
Requester pays access isn't working
Error in the cleanHardClippedCigar function ClippingOp class
VariantAnnotator fails to generate correct reference-based annotations
Spark SV pipeline example shell scripts currently not working
Ambiguous results with HaplotypeCaller output modes EMIT_ALL_CONFIDENT_SITES and EMIT_ALL_SITES
GATK HaplotypeCaller reports nonsense GT/AD when --min-base-quality-score parameter changes
GATK4 Funcotator generated annotation differs from dbSNP
Add better error message when Java is not installed to the launch script
Funcotator datasource configs should not honor spaces (and some other special characters) in the datasource name nor version.
Warnings should include info about their source
SortSam ShardedInput tests failing.
BaseRecalibratorSpark fails with "java.lang.IllegalArgumentException: Table1 1,3 not equal to 88,3"
Problem with BaseRecalibrator: java.lang.IllegalArgumentException: fromIndex(64) > toIndex(62)
Intel deflater + long reads data = intermittent corrupt bams
GenotypeGVCFs not outputting some variants it should with -stand-call-conf
Funcotator reproducibly crashes on specific WES VCF record produced by GATK4.1.0 (java 1.8.0_45)
Wrong center locations in BandPassActivityProfile
AnalyzeCovariates produces invalid csv when readgroups contain commas, resulting in a crash
GenotypeGvcfs mangles the input phase