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1,237 Open 3,353 Closed
1,237 Open 3,353 Closed
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Issues list

PostprocessGermlineCNVCalls outputs wrong genotyped-segments results
#9111 opened Mar 4, 2025 by DiabloRex
Hardcoded HTSJDK JEXL genotype filter bindings not working as expected for VariantFiltration.
#9108 opened Mar 3, 2025 by gokalpcelik
GATK4.5.0.0 HaplotypeCaller exits with error code 245 while no error message
#9104 opened Feb 28, 2025 by Alipha-Clisa
GtfToBed errors out with because "gene" is null
#9103 opened Feb 27, 2025 by mmahmoudian
2
Efficiently perform simple merge/append on many VCFs?
#9097 opened Feb 18, 2025 by bbimber
4
negative CNN_1D scores
#9088 opened Feb 4, 2025 by MarionFresquet
2
Miscalling of SNPs and GQ value of 0
#9086 opened Feb 3, 2025 by Sgornard
9
Docker 4.6.1.0 image not finding includes
#9084 opened Jan 24, 2025 by pjgreer
1
FilterAlignmentArtifacts - Padded span must contain active span
#9075 opened Jan 14, 2025 by dansteiert
macOS install
#9074 opened Jan 13, 2025 by BenjaminDEMAILLE
1
Homebrew
#9073 opened Jan 13, 2025 by BenjaminDEMAILLE
2
Problem in gvcf interplay between clair3 and gatk
#9068 opened Jan 6, 2025 by johannesgeibel
1
VariantAnnotator giving error "No overlapping contigs found"
#9067 opened Jan 3, 2025 by khanshahan
1
Variant annotator step in jointcalling procedure
#9064 opened Dec 24, 2024 by SiddhiJani
java with conda install
#9063 opened Dec 19, 2024 by stuartwillis
python exited with 1. Theano error.
#9062 opened Dec 12, 2024 by lovelycatZ
1
GATK 4.6. SelectVariants not applying --select filters
#9060 opened Dec 9, 2024 by FLsandell
1
FilterIntervals will get rid of Y chromosome intervals if there are >50% of female samples
#9043 opened Nov 14, 2024 by NotAPoetButACriminal
2
Enabling PDHMM causes GVCF mode to fail.
#9041 opened Nov 13, 2024 by gokalpcelik
1
Issue Running GATK Mitochondrial Pipeline
#9037 opened Nov 11, 2024 by jingxiant
PON filtering logic and tag in vcf.gz file
#9035 opened Nov 7, 2024 by YuanTian1991
0 or 1 based coordinates.
#9029 opened Oct 31, 2024 by vappiah
1
Why is it possible to visualize a mutation at a specific locus in the BAM file in IGV, but cannot be called using mutect2?
#9021 opened Oct 29, 2024 by Joyjoyjoyc
Add hap.py/som.py benchmarking results to docs for each release
#9019 opened Oct 25, 2024 by skchronicles
Handling low bases in AD calculation question
#9014 opened Oct 21, 2024 by pogodina-nadezda
1
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