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varfish-org
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varfish-annotator
(Legacy) Annotate variants for import into VarFish server.
MIT License
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chore: common .github files
#101
holtgrewe
opened
9 months ago
0
Fixing problem with left-trimming variants (#99)
#100
holtgrewe
closed
1 year ago
0
Problem with REF/ALT normalization in VCF
#99
holtgrewe
closed
1 year ago
0
VCF file looks like hg37 by chr1 length you required GRCh38 error
#98
Saranya-Balachandran
closed
1 year ago
2
Add explicit support for PopDel
#97
holtgrewe
opened
1 year ago
0
Fixing bug when annotating MELT with missing AD (#95).
#96
holtgrewe
closed
1 year ago
0
NPE when annotating MELT results
#95
holtgrewe
closed
1 year ago
0
Interpret FORMAT/SQ as Float (#93)
#94
holtgrewe
closed
1 year ago
0
Exception in thread "main" java.lang.NumberFormatException: For input string: "21.44"
#93
Nicolai-vKuegelgen
closed
1 year ago
0
Adding support for MELT (#91)
#92
holtgrewe
closed
1 year ago
0
Make sure that we can annotate MELT VCFs
#91
holtgrewe
closed
1 year ago
0
Implement release-please
#90
holtgrewe
opened
1 year ago
0
fix: Delly2 VCF files work now when merging SV VCF files (#88)
#89
holtgrewe
closed
1 year ago
0
NPE when annotating Delly2 files
#88
holtgrewe
closed
1 year ago
1
84 handle absent quality metrics for mt coming from dragen
#87
holtgrewe
closed
1 year ago
0
Suppress BND records that point to non-allow-listed contigs (#85).
#86
holtgrewe
closed
1 year ago
0
Remove BND with non-included target sequences
#85
holtgrewe
closed
1 year ago
0
Handle absent quality metrics for MT coming from DRAGEN
#84
eudesbarbosa
closed
1 year ago
1
Write out SV callers as array (#81)
#83
holtgrewe
closed
2 years ago
1
Write out SV callers as array (#81)
#82
holtgrewe
closed
2 years ago
0
Write out SV callers as array
#81
holtgrewe
closed
2 years ago
0
79 ensure output is always sorted
#80
holtgrewe
closed
2 years ago
0
Ensure output is always sorted
#79
holtgrewe
closed
2 years ago
0
Merge multiple input VCFs in annotate-svs with clustering (#75)
#78
holtgrewe
closed
2 years ago
0
Adding support to annotate CNVs with DoC (#73)
#77
holtgrewe
closed
2 years ago
1
Fixing SVTYPE=CNV for DRAGEN CNV (#74)
#76
holtgrewe
closed
2 years ago
1
Implement support for handling multiple VCF files in annotate-svs
#75
holtgrewe
closed
2 years ago
0
Write out DEL/DUP from DRAGEN CNV calling as SVTYPE={DEL,DUP}
#74
holtgrewe
closed
2 years ago
0
Implement support for annotating depth of coverage and mapping quality for CNVs
#73
holtgrewe
closed
2 years ago
0
Add explicit support for SV calling tools (#68)
#72
holtgrewe
closed
2 years ago
1
Remove support for anthenea-only headers
#71
holtgrewe
opened
2 years ago
0
Removing explicit support for SV2 (#67)
#70
holtgrewe
closed
2 years ago
0
Add support for Delly2 CNV and MELT
#69
holtgrewe
opened
2 years ago
0
Add explicit support for SV calling tools
#68
holtgrewe
closed
2 years ago
0
Remove explicit support for SV2
#67
holtgrewe
closed
2 years ago
0
Properly document and test supported callers (#65)
#66
holtgrewe
closed
2 years ago
0
Run on real caller output in tests
#65
holtgrewe
closed
2 years ago
1
Increasing test coverage (#63)
#64
holtgrewe
closed
2 years ago
1
Increase test coverage
#63
holtgrewe
closed
2 years ago
0
Adding end-to-end tests hg19-chr22 (#61)
#62
holtgrewe
closed
2 years ago
0
Add system/end-to-end tests for varfish-annotator
#61
holtgrewe
closed
2 years ago
0
`IndexOutOfBoundsException` and `MissingSVTypeInfoField` for DRAGEN CNV VCF
#60
eudesbarbosa
closed
2 years ago
0
Preparing v0.25 release (#58)
#59
holtgrewe
closed
2 years ago
0
Release v0.25
#58
holtgrewe
closed
2 years ago
0
Fixing unresolved issue with self-test (#51, #56)
#57
holtgrewe
closed
2 years ago
0
Sanity check for GRCh37 gnomad genomes and chromosome "Y" is wrong
#56
holtgrewe
closed
2 years ago
0
Release v0.24
#55
holtgrewe
closed
2 years ago
0
Suppress writing out `*Carriers` for SVs by default (#53)
#54
holtgrewe
closed
2 years ago
0
Do not write out {unaffected,affected,background}Carriers into INFO field for structural variants TSV
#53
holtgrewe
closed
2 years ago
1
Fixing self-test on gnomAD genomes with chrY (#51)
#52
holtgrewe
closed
2 years ago
1
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