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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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RW-14014 Fix vpcError in wdl
#9053
Qi77Qi
opened
1 hour ago
0
Joel gsutil
#9052
jmthibault79
opened
1 day ago
0
Sample chromosome ploidy support for RWB Echo [VS-1500]
#9051
mcovarr
opened
1 day ago
2
Update docs for moved script [VS-1490]
#9050
mcovarr
closed
2 days ago
0
VS-1514 backwards compatibility
#9049
gbggrant
opened
2 days ago
1
Prepare for release of GVS 0.6.1 / RWB Echo [VS-1500]
#9048
mcovarr
closed
2 days ago
0
Update README.md
#9047
gokalpcelik
closed
2 days ago
0
VariantRecalibrator R script fix for recent R versions.
#9046
gokalpcelik
closed
3 days ago
0
[DO NOT MERGE]
#9045
jamesemery
opened
1 week ago
3
VS-1515 - Passing ploidy_table_name into GvsExtractCallset.wdl
#9044
gbggrant
closed
1 week ago
0
FilterIntervals will get rid of Y chromosome intervals if there are >50% of female samples
#9043
NotAPoetButACriminal
opened
1 week ago
2
Dockstore bugfix
#9042
RoriCremer
closed
2 days ago
1
Enabling PDHMM causes GVCF mode to fail.
#9041
gokalpcelik
opened
1 week ago
0
Running tests
#9040
lbergelson
closed
1 week ago
3
VS 1528 Update the sharding of the samples in the VAT creation to be dependent on the number of samples
#9039
RoriCremer
closed
23 hours ago
0
'Cannot read non-existent file' issue related to incorrect parsing of paths
#9038
jphruska
closed
6 days ago
3
Issue Running GATK Mitochondrial Pipeline
#9037
jingxiant
opened
1 week ago
0
RW-11727 pass query_project instead
#9036
Qi77Qi
closed
1 week ago
0
PON filtering logic and tag in vcf.gz file
#9035
YuanTian1991
opened
2 weeks ago
0
VS-1526 - Fix error in Extract Manifest Creation causing it to run forever.
#9034
gbggrant
closed
1 week ago
0
Maximum alt alleles guardrail [VS-1530]
#9033
mcovarr
closed
6 days ago
0
Retain all source IDs on VariantContext merge + test
#9032
bbimber
closed
1 week ago
2
Port of `CallableLoci` from GATK3
#9031
jonn-smith
closed
1 week ago
1
Genotype Discrepancy Between Individual and Merged GVCF Files Using GATK
#9030
jiangluguang123
closed
1 week ago
0
0 or 1 based coordinates.
#9029
vappiah
opened
3 weeks ago
1
Base cohort extract scatter width on loaded sample count [VS-1513]
#9028
mcovarr
closed
2 weeks ago
0
Yyu test 1
#9026
yonghaoy
opened
3 weeks ago
0
optional column call_ps
#9025
yonghaoy
opened
3 weeks ago
0
GenomicsDBImport and CombineGVCFs results don't match
#9024
gokalpcelik
opened
3 weeks ago
0
pass dest project id
#9023
yonghaoy
closed
3 weeks ago
2
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
Joyjoyjoyc
opened
3 weeks ago
0
BQSR: avoid throwing an error when read group is missing in the recal table, and some refactoring.
#9020
takutosato
opened
3 weeks ago
2
Add hap.py/som.py benchmarking results to docs for each release
#9019
skchronicles
opened
4 weeks ago
0
Change the kryo version specification to use maven style [,) instead of +
#9018
lbergelson
closed
4 weeks ago
0
VS-1490 - Refactor python code from extract dir into a scripts directory.
#9017
gbggrant
closed
1 week ago
0
Use jetty bom to enforce uniform jetty versions
#9016
lbergelson
closed
1 month ago
0
VS-1476. Removing All usage of VQSR from VDS creation.
#9015
gbggrant
closed
3 weeks ago
0
Handling low bases in AD calculation
#9014
pogodina-nadezda
opened
1 month ago
1
Potential Mismatch between the MAF output mode and VCF output mode on Gencode V43
#9013
jamesemery
opened
1 month ago
0
Added a '--prefer-mane-transcripts' mode that enforces MANE_Select tagged Gencode transcripts where possible
#9012
jamesemery
closed
1 month ago
1
Hook up the Python-based unit tests for NVScoreVariants to our test suite
#9011
droazen
opened
1 month ago
0
Mark NVScoreVariants as a beta feature
#9010
droazen
closed
1 month ago
0
Remove CNNScoreVariants, CNNVariantTrain, and CNNVariantWriteTensors
#9009
droazen
closed
1 month ago
1
Adding small warning messages to not to feed any GVCF files to these tools
#9008
gokalpcelik
closed
1 month ago
0
Possible bug in GenotypeGVCFs 4.6.0.0, affecting all genotyping applications
#9007
gevro
opened
1 month ago
6
Additional Dependency updates
#9006
lbergelson
closed
1 month ago
3
Update docker base
#9005
lbergelson
closed
1 month ago
0
Bump com.google.protobuf:protobuf-java from 3.23.4 to 3.25.5
#9004
dependabot[bot]
closed
1 month ago
2
Bump commons-io:commons-io from 2.7 to 2.14.0
#9003
dependabot[bot]
closed
1 month ago
1
Add dependency submission workflow so we can monitor vulnerabilities
#9002
lbergelson
closed
1 month ago
0
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