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broadinstitute
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gatk
Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Add more detailed conda setup instructions to the GATK README
#9001
droazen
closed
1 month ago
1
Re-added `--only-output-calls-starting-in-intervals` as a deprecated argument with warning.
#9000
jamesemery
closed
1 month ago
0
Update Mutect2.java Documentation
#8999
gokalpcelik
closed
1 month ago
0
Update gradle and build.gradle
#8998
lbergelson
closed
1 month ago
2
Feature Request: Progress Bar Estimated Time Remaining
#8997
jonn-smith
opened
1 month ago
0
Create tools for SV VCF cleaning
#8996
kjaisingh
opened
1 month ago
0
Base-specific Phred score filtering/output options in AnalyzeSaturationMutagenesis
#8995
BenjaminWehnert1008
opened
1 month ago
1
Vs 1416 modify ingest to correctly handle ploidy differences in dragen 3 7 8 samples
#8994
koncheto-broad
closed
2 weeks ago
9
VS-1506 - Pull changes from EchoCallset into ah_var_store branch
#8993
gbggrant
closed
1 month ago
0
Update VariantRecalibrator RScript Compatibility with Newer ggplot2 Versions
#8992
Nanderson246
opened
1 month ago
1
VS-1288 Updates to ah_var_store from echo callset.
#8991
gbggrant
closed
1 month ago
0
Add SVStratify and GroupedSVCluster tools
#8990
mwalker174
closed
4 days ago
0
Memory leak in GenotypeGVCFs with `-all-sites`
#8989
brisk022
opened
1 month ago
8
SIGSEGV when running gatk/4.6.0.0
#8988
emwjacobson
opened
1 month ago
6
Switch to logging a warning instead of an exception for intervals in query that were not part of GenomicsDBImport
#8987
nalinigans
closed
1 month ago
0
Swapped mito mode in Mutect to use the mode argument utils
#8986
jamesemery
closed
1 month ago
0
Change Batch Size Parameter to Scatter Width For Ingest [VS-1218]
#8985
rsasch
closed
1 month ago
0
Haplotypecaller error
#8984
polymerase2010
closed
2 months ago
2
How to filter on funcotation subfields
#8983
keenhl
opened
2 months ago
0
FlowFeatureMapper speed improvements
#8982
dror27
opened
2 months ago
3
Update cleanup doc [VS-787]
#8981
rsasch
closed
2 months ago
0
Add a few additional failures to our notes doc
#8980
RoriCremer
opened
2 months ago
2
Tweak extract values based on Echo Runs [VS-1432]
#8979
rsasch
closed
2 months ago
5
Adds QD and AS_QD emission from VariantAnnotator on GVS input
#8978
meganshand
closed
2 months ago
0
VS-1422 Merge VAT changes in echo into ah_var_store
#8977
gbggrant
closed
1 month ago
0
Update Docs Around Callset Cleanup and Cost [VS-1107]
#8976
rsasch
closed
2 months ago
0
LeftAlignIndels Alignments added out of order issue when reads are fed in coordinate sorted order.
#8975
gokalpcelik
opened
2 months ago
0
gVCF ALT Column Showing Only <NON_REF>
#8974
kotchanipar
opened
2 months ago
0
Updates to VcfComparator
#8973
meganshand
closed
1 month ago
0
Echo callset
#8972
gbggrant
closed
2 months ago
0
Update CRAM detector output files.
#8971
cmnbroad
closed
2 months ago
0
Gg vs 1990 a widdle cleanup
#8970
gbggrant
closed
1 month ago
0
GenotypeGVCFs error in GATK 4.6.0.0: java.lang.RuntimeException: Invalid deflate block found.
#8969
hxtjc
opened
2 months ago
0
VS-1485 - Optionally call CollectVariantCallingMetrics from ExtractVcfs
#8968
gbggrant
closed
2 months ago
0
VS-1483 Update AoU documentation to include details for VAT delivery
#8967
gbggrant
closed
2 months ago
0
WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
#8966
ChrisSteel-bio
opened
2 months ago
0
Strange output by Funcotator
#8965
gevro
opened
2 months ago
2
VariantFiltration failed
#8964
Wasya-the-Wolf
opened
2 months ago
2
Funcotator: all Clinvar fields blank
#8963
gevro
opened
2 months ago
3
Require both overlap and breakend proximity for depth-only SV clustering
#8962
mwalker174
closed
2 months ago
2
HaplotypeCallerSpark Failed because GenotypesCache thrown NPE
#8961
Xuehai-Chen
opened
3 months ago
2
VS-1466 restructure export vcf for copy reasons
#8960
gbggrant
closed
2 months ago
0
Inconsistent Handling of Artificial Reads in Allele Depth (AD) Calculation
#8959
mrymkdnz
closed
2 months ago
8
VS-1470 Have Extract Cohort to PGEN write to cost_observability table
#8958
gbggrant
closed
3 months ago
1
FlowFeatureMapper optimization
#8957
dror27
closed
2 months ago
0
Discrepancy Between IGV and VCF File for HaplotypeCaller
#8956
mrymkdnz
closed
3 months ago
4
Slight AoU docs adjustment [VS-1366]
#8955
mcovarr
closed
3 months ago
0
Update Script to Handle Both Files and FOFN [VS-1441]
#8954
rsasch
closed
3 months ago
0
alt allels error
#8953
gaochenx
opened
3 months ago
1
Convergence Error running GATK GermlineCNVCaller cohort mode
#8952
snakesch
opened
3 months ago
5
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