issues
search
broadinstitute
/
gatk
Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
Other
1.62k
stars
575
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Docker untangling [VS-1279]
#8805
mcovarr
closed
1 month ago
0
X_FILTERED_COUNT semantics adjusted
#8804
dror27
closed
1 month ago
0
VS-1310. Update gatk docker on EchoCallset
#8803
gbggrant
closed
1 month ago
0
Add malaria spanning deletion exception regression test with fix
#8802
ldgauthier
closed
1 month ago
0
VS-1356 - Update docker from master
#8801
gbggrant
closed
1 month ago
0
VariantAnnotator IndexOutOfBoundsException
#8800
ykcchong
opened
1 month ago
0
Added long read walkers from long-running branch.
#8799
jonn-smith
opened
1 month ago
1
VS-1310 Optionally convert filtered genotypes to no-calls (#8793)
#8798
gbggrant
closed
1 month ago
0
VS-1310 - VS-1310 changes to echo callset branch
#8797
gbggrant
closed
1 month ago
0
Moving some long read tools into GATK from a long-standing branch
#8796
jonn-smith
closed
1 month ago
3
VS-1341 Improve test cost calculation
#8795
gbggrant
closed
3 weeks ago
0
Vat pipeline--Even more juice
#8794
RoriCremer
closed
1 month ago
0
VS-1310 Optionally convert filtered genotypes to no-calls
#8793
gbggrant
closed
1 month ago
1
PLINK2 Docker [VS-1315]
#8792
mcovarr
closed
1 month ago
0
Fix GAR support [VS-1342]
#8791
mcovarr
closed
1 month ago
1
repartition tables before merge
#8790
RoriCremer
closed
1 month ago
1
Revert explicit GAR references for now [VS-1342]
#8789
mcovarr
closed
1 month ago
1
Prevent users enabling annotations with mismatching data type (flow etc)
#8788
gokalpcelik
opened
1 month ago
7
VS-1324 Investigate integration test failures
#8787
gbggrant
closed
1 month ago
0
Some temporary hacks to restart VAT sites-only VCF writing
#8786
mcovarr
closed
1 month ago
3
⛔ [DO NOT MERGE] ⛔ Fix partition grouping bug ⛔
#8785
mcovarr
opened
1 month ago
0
Add Konrad's changes
#8784
RoriCremer
closed
1 month ago
1
Docker image ID in tags [VS-1340]
#8783
mcovarr
closed
1 month ago
1
switch back to standard workers
#8782
RoriCremer
closed
1 month ago
0
Gc getpipeupsummaries use mappingqualityreadfilter
#8781
gokalpcelik
closed
1 month ago
1
Limit the number of parts we run the VAT pipeline on as a test
#8780
RoriCremer
closed
1 month ago
1
PGEN / VCF tieout [VS-1311]
#8779
mcovarr
closed
1 month ago
0
Rc vs 903 tighten hail code
#8778
RoriCremer
closed
1 month ago
1
GenotypeGVCFs report java.lang.OutOfMemoryError: Java heap space while call incremental imported GenomicsDB
#8777
LYOKOIIIYYR
opened
1 month ago
3
PostprocessGermlineCNVCalls error
#8776
lovelycatZ
closed
1 month ago
2
Bug fix in flow allele filtering
#8775
ilyasoifer
closed
1 month ago
1
Better hail comments
#8774
RoriCremer
closed
1 month ago
1
VS-1336 - It's not a site FILTER
#8773
gbggrant
closed
2 weeks ago
0
Update hail_create_vat_inputs.py
#8772
konradjk
closed
1 month ago
0
Enable ReblockGVCF to subset AS annotations that aren't "raw" (pipe-delimited)
#8771
ldgauthier
closed
1 month ago
1
add logging and validate vat to echo callset branch
#8770
RoriCremer
closed
1 month ago
0
Change large test files from PR 8741 to lfs
#8769
lbergelson
closed
1 month ago
0
PrintReads introduces N bases when encoding some CRAMs and changes sequence
#8768
ilyasoifer
opened
1 month ago
14
ApplyVQSR Exception thrown at a/some variation site(s) after INDEL VQSR
#8767
Dkyuan
opened
1 month ago
0
Using PathSeqFilterSpark --ignore-alignment-contigs raises error
#8766
abdohlman
opened
1 month ago
0
Make CreateTables volatile [VS-1328]
#8765
rsasch
closed
1 month ago
0
Use `noAddress` to limit use of external IPs [VS-1323]
#8764
mcovarr
closed
1 month ago
1
noAddress experiment
#8763
mcovarr
closed
1 month ago
0
hail updates
#8762
RoriCremer
closed
1 month ago
0
hardcode bigger main machine
#8761
RoriCremer
closed
1 month ago
0
Docs for monitoring quotas and requesting increases [VS-1320]
#8760
rsasch
closed
1 month ago
0
Allow for GT to be a nocall if GQ and PL[0] are zero instead of homref in GenomicsDB
#8759
nalinigans
closed
3 weeks ago
8
Funcotator: suppress a log message about b37 contigs when not doing b37/hg19 conversion
#8758
droazen
closed
2 months ago
0
add echocallset as an option for integration test
#8757
RoriCremer
opened
2 months ago
0
Introduce more rationalized date model for the GATK logger output
#8756
jamesemery
closed
2 months ago
2
Previous
Next