Related Issues (20)
- SplitNCigarReads.java - retain original read name somewhere for split parts of reads so we know where it derived from. HOT 10
- GenotypeGVCFs - A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader HOT 1
- Bug Funcotator: wrong canonical HOT 1
- SelectVariants (Documentation): Purpose of reference sequence
- Multiple Tools (Documentation): Format of `--arguments_file`
- Memory issues when running BaseRecalibrator
- Add toggle for treatment of MNPs in VETS.
- java.io.IOException: Transport endpoint is not connected
- GCNV: AssertionError: Loaded mean for "log_mean_bias_t" has an unexpected shape; loaded: (11903,), expected: (11901,)
- How to avoid java.lang.ArrayIndexOutOfBoundsException when indexing a vcf.gz file?
- GATK VariantsToTable: QUAL="." in input becomes QUAL="-10.0" in output
- Bug in NIO library using public reference files ending in .fa.gz
- Using PathSeqFilterSpark --ignore-alignment-contigs raises error
- ApplyVQSR Exception thrown at a/some variation site(s) after INDEL VQSR
- PrintReads introduces N bases when encoding some CRAMs and changes sequence HOT 15
- PostprocessGermlineCNVCalls error HOT 2
- GenotypeGVCFs report java.lang.OutOfMemoryError: Java heap space while call incremental imported GenomicsDB HOT 3
- Prevent users enabling annotations with mismatching data type (flow etc) HOT 7
- VariantAnnotator IndexOutOfBoundsException
- [bug report] CNNScoreVariants can't continue HOT 1
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