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).

Showing open

Error in the cleanHardClippedCigar function ClippingOp class
M2 error with canine germline resource and variants_for_contamination files
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
HaplotypeCaller --output-mode EMIT_ALL_SITES does not 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
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
Bug in HaplotypeCaller: lack of consistency in the overlap criteria applied to reads to be considered for PL and AD/DP annotations.