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1,224 Open 3,344 Closed
1,224 Open 3,344 Closed
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Issues list

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
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
GenomicsDBImport and CombineGVCFs results don't match
#9024 opened Oct 30, 2024 by gokalpcelik
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
Potential Mismatch between the MAF output mode and VCF output mode on Gencode V43
#9013 opened Oct 18, 2024 by jamesemery
Hook up the Python-based unit tests for NVScoreVariants to our test suite Python tests
#9011 opened Oct 18, 2024 by droazen
@lbergelson
Possible bug in GenotypeGVCFs 4.6.0.0, affecting all genotyping applications
#9007 opened Oct 17, 2024 by gevro
6
Feature Request: Progress Bar Estimated Time Remaining
#8997 opened Oct 10, 2024 by jonn-smith
Base-specific Phred score filtering/output options in AnalyzeSaturationMutagenesis
#8995 opened Oct 9, 2024 by BenjaminWehnert1008
1
Update VariantRecalibrator RScript Compatibility with Newer ggplot2 Versions
#8992 opened Oct 3, 2024 by Nanderson246
1
Memory leak in GenotypeGVCFs with -all-sites bug GenomicsDB
#8989 opened Oct 1, 2024 by brisk022
@nalinigans
8
SIGSEGV when running gatk/4.6.0.0 bug GKL
#8988 opened Sep 30, 2024 by emwjacobson
6
How to filter on funcotation subfields
#8983 opened Sep 17, 2024 by keenhl
LeftAlignIndels Alignments added out of order issue when reads are fed in coordinate sorted order.
#8975 opened Sep 9, 2024 by gokalpcelik
gVCF ALT Column Showing Only <NON_REF>
#8974 opened Sep 9, 2024 by kotchanipar
GenotypeGVCFs error in GATK 4.6.0.0: java.lang.RuntimeException: Invalid deflate block found.
#8969 opened Sep 3, 2024 by hxtjc
WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
#8966 opened Aug 28, 2024 by ChrisSteel-bio
Strange output by Funcotator
#8965 opened Aug 27, 2024 by gevro
2
VariantFiltration failed
#8964 opened Aug 27, 2024 by Wasya-the-Wolf
2
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