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Issues list

GtfToBed errors out with because "gene" is null
#9103 opened Feb 27, 2025 by mmahmoudian updated Feb 27, 2025
Efficiently perform simple merge/append on many VCFs?
#9097 opened Feb 18, 2025 by bbimber updated Feb 18, 2025
Docker 4.6.1.0 image not finding includes
#9084 opened Jan 24, 2025 by pjgreer updated Feb 17, 2025
Miscalling of SNPs and GQ value of 0
#9086 opened Feb 3, 2025 by Sgornard updated Feb 13, 2025
negative CNN_1D scores
#9088 opened Feb 4, 2025 by MarionFresquet updated Feb 7, 2025
macOS install
#9074 opened Jan 13, 2025 by BenjaminDEMAILLE updated Feb 4, 2025
Enabling PDHMM causes GVCF mode to fail.
#9041 opened Nov 13, 2024 by gokalpcelik updated Jan 15, 2025
FilterAlignmentArtifacts - Padded span must contain active span
#9075 opened Jan 14, 2025 by dansteiert updated Jan 14, 2025
Homebrew
#9073 opened Jan 13, 2025 by BenjaminDEMAILLE updated Jan 13, 2025
Problem in gvcf interplay between clair3 and gatk
#9068 opened Jan 6, 2025 by johannesgeibel updated Jan 6, 2025
VariantAnnotator giving error "No overlapping contigs found"
#9067 opened Jan 3, 2025 by khanshahan updated Jan 6, 2025
Variant annotator step in jointcalling procedure
#9064 opened Dec 24, 2024 by SiddhiJani updated Dec 24, 2024
java with conda install
#9063 opened Dec 19, 2024 by stuartwillis updated Dec 19, 2024
python exited with 1. Theano error.
#9062 opened Dec 12, 2024 by lovelycatZ updated Dec 12, 2024
GATK 4.6. SelectVariants not applying --select filters
#9060 opened Dec 9, 2024 by FLsandell updated Dec 9, 2024
VariantRecalibrator R-script fails if scales v1.3.0 is installed bug
#8664 opened Jan 23, 2024 by MikkelSchubert updated Nov 20, 2024
1 of 2 tasks
Could not load genomicsdb native library GenomicsDB
#4124 opened Jan 11, 2018 by owensgl updated Nov 19, 2024
Issue Running GATK Mitochondrial Pipeline
#9037 opened Nov 11, 2024 by jingxiant updated Nov 11, 2024
Memory issues when running BaseRecalibrator
#8726 opened Mar 9, 2024 by MetteBoge updated Nov 11, 2024
PON filtering logic and tag in vcf.gz file
#9035 opened Nov 7, 2024 by YuanTian1991 updated Nov 7, 2024
0 or 1 based coordinates.
#9029 opened Oct 31, 2024 by vappiah updated Nov 1, 2024
ProTip! Updated in the last three days: updated:>2025-02-24.