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broadinstitute
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seqr-loading-pipelines
hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
MIT License
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Filter NON_REF and raise a validation error if there are other SNV_IN…
#884
bpblanken
opened
1 hour ago
0
VEP Config update
#883
bpblanken
opened
5 hours ago
0
add stricter AF prefilter option
#882
hanars
opened
7 hours ago
1
Benb/wrap import methods in validation
#881
bpblanken
opened
9 hours ago
0
main into dev
#880
jklugherz
closed
1 week ago
0
Dev
#879
jklugherz
closed
1 week ago
1
Fix liftover caching bug in tests
#878
bpblanken
closed
1 week ago
0
Make sure WriteMetadataForRunTask is always in the dependency tree
#877
bpblanken
closed
1 week ago
0
Local Pipeline `api` and `worker`
#876
bpblanken
closed
1 day ago
0
some inheritance refactoring
#875
bpblanken
closed
1 week ago
0
Remove reference data env var
#874
bpblanken
closed
1 week ago
0
Dev
#873
bpblanken
closed
2 weeks ago
0
Dev
#872
jklugherz
closed
2 weeks ago
0
Delete ONT data
#871
lynnpais
closed
1 week ago
1
Move sex checks out of data loading pipeline
#870
lynnpais
opened
2 weeks ago
0
Bump aiohttp from 3.9.4 to 3.10.2
#869
dependabot[bot]
closed
2 weeks ago
0
lookup table pipeline logic uses sample_type
#868
jklugherz
closed
1 week ago
0
lookup sample_type migration
#867
jklugherz
closed
1 week ago
0
Benb/migration3
#866
bpblanken
closed
2 weeks ago
0
Add `strvctvre` annotation.
#865
bpblanken
opened
3 weeks ago
0
Benb/rg38 locus
#864
bpblanken
closed
2 weeks ago
0
Re-architect `lookup` table (yet again!)
#863
bpblanken
opened
3 weeks ago
0
Add tests for the implemented migrations.
#862
bpblanken
opened
3 weeks ago
0
Bump scikit-learn from 1.3.2 to 1.5.0
#861
dependabot[bot]
closed
3 weeks ago
0
main <- dev
#860
bpblanken
closed
3 weeks ago
0
Pipeline should check the integrity of the metadata.json generated during a run.
#859
bpblanken
opened
4 weeks ago
1
Add a task to export the SV annotations table to VCF.
#858
bpblanken
closed
4 weeks ago
0
Add new SV annotations for VCF export.
#857
bpblanken
closed
4 weeks ago
0
Resolve the assumption in the pipeline that remap/pedigree files are immutable.
#856
bpblanken
closed
3 weeks ago
0
Benb/add alleles annotation svs
#855
bpblanken
closed
4 weeks ago
0
Pipeline `complete()` needs to consider pedigree/remap information.
#854
bpblanken
closed
3 weeks ago
1
Audit of Sample QC Genetic Ancestry Imputation on gnomAD v2+CMG vs gnomAD v4 Model
#853
matren395
opened
1 month ago
0
Modest Audit of DRAGEN Sample QC Outputs
#852
matren395
opened
1 month ago
0
Audit Sample QC Fields.
#851
bpblanken
opened
1 month ago
1
Import DRAGEN metrics file into v03 pipeline.
#850
bpblanken
opened
1 month ago
0
Map fields produced by seqr sample qc pipeline to UI fields in seqr.
#849
bpblanken
opened
1 month ago
0
Add automated docker builds to CI
#848
bpblanken
opened
1 month ago
0
Dev
#847
bpblanken
closed
1 month ago
0
Remove `high_constraint_region_mito`
#846
bpblanken
opened
1 month ago
0
Add mito local constraint
#845
bpblanken
closed
1 month ago
0
Move VEP files from a `110` path to `GRCh38`.
#844
bpblanken
closed
1 month ago
0
VLM
#843
lynnpais
opened
1 month ago
0
add sample_type to family and project table paths
#842
jklugherz
closed
2 weeks ago
1
New pipeline runner image.
#841
bpblanken
closed
2 weeks ago
0
Checkpoint no longer necessary with improved caching
#840
bpblanken
closed
1 month ago
0
Dev
#839
bpblanken
closed
1 month ago
0
Intersect family guids when determining which to load
#838
bpblanken
closed
1 month ago
0
Family Table write needs to consider the pedigree when determining which families to update.
#837
bpblanken
closed
1 month ago
2
Benb/lookup optimization
#836
bpblanken
closed
1 month ago
0
Benb/split import and validate (#829)
#835
bpblanken
closed
1 month ago
0
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