Skip to content

Issues: broadinstitute/gatk

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

1,223 Open 3,344 Closed
1,223 Open 3,344 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

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
Funcotator: all Clinvar fields blank
#8963 opened Aug 26, 2024 by gevro
3
ProTip! Adding no:label will show everything without a label.