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broadinstitute
/
seqr-loading-pipelines
hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
MIT License
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Benb/split import and validate
#829
bpblanken
opened
4 days ago
0
Callset Import failure due to out of order keys.
#828
bpblanken
opened
4 days ago
3
Fix field references
#827
bpblanken
closed
6 days ago
0
update biotype and consequence enums ids (#825)
#826
bpblanken
closed
6 days ago
1
update biotype and consequence enums ids
#825
bpblanken
closed
1 week ago
0
fix additional location
#824
bpblanken
closed
1 week ago
0
Use the `ETag` of the clinvar submission and vcf to cache our gcs temp files.
#823
bpblanken
opened
1 week ago
0
Audit/Reorganize v03_pipeline feature flags.
#822
bpblanken
opened
1 week ago
0
Create a simple http interface that responds to http POSTs and kicks off the v03_pipeline.
#821
bpblanken
opened
1 week ago
0
Create an updated pipeline-runner docker image that includes new VEP dependencies and v03_pipeline code.
#820
bpblanken
opened
1 week ago
0
add it back
#819
jklugherz
closed
1 week ago
0
use_new_shuffle=None
#818
jklugherz
closed
1 week ago
0
unzip submission summary before join (#816)
#817
bpblanken
closed
1 week ago
0
unzip submission summary before join
#816
jklugherz
closed
1 week ago
0
biotype enums
#815
bpblanken
closed
1 week ago
1
use predetermined filters/imputed_sex paths
#814
bpblanken
closed
2 weeks ago
0
warnings file
#813
bpblanken
closed
3 weeks ago
0
VEP migration.
#812
bpblanken
closed
2 weeks ago
0
Add an extra `hl.eval` when computing which families to preserve.
#811
bpblanken
closed
1 week ago
0
tweak logic to prefer filter
#810
bpblanken
closed
3 weeks ago
0
Parameter refactoring + cleanup.
#809
bpblanken
closed
6 days ago
0
Split "SampleType" out from shared task base class.
#808
bpblanken
closed
2 weeks ago
0
Remove concept of private crdqs
#807
bpblanken
closed
3 weeks ago
1
Bump msal from 1.25.0 to 1.28.0
#806
dependabot[bot]
closed
3 weeks ago
0
Bump azure-identity from 1.15.0 to 1.16.1
#805
dependabot[bot]
closed
3 weeks ago
0
Dev
#804
bpblanken
closed
3 weeks ago
0
remove "ignore_missing_samples_when_subsetting"
#803
bpblanken
closed
3 weeks ago
0
Bump tornado from 6.3.3 to 6.4.1
#802
dependabot[bot]
closed
3 weeks ago
0
Add ensembl to refseq transcript id mapping.
#801
bpblanken
closed
1 month ago
0
Add Ensembl -> Refseq lookup to "write_new_variants_table"
#800
bpblanken
closed
1 week ago
1
clear globals on new variants table
#799
bpblanken
closed
1 month ago
0
Add Type Assertions to imported fields.
#798
bpblanken
closed
3 weeks ago
0
Import fields with fully qualified names.
#797
bpblanken
closed
3 weeks ago
0
main <- dev
#796
bpblanken
closed
1 month ago
0
Support unknowns in pedigree
#795
bpblanken
closed
1 month ago
0
Pedigree/S&R Cleanup
#794
bpblanken
closed
1 month ago
1
main <- dev
#793
jklugherz
closed
1 month ago
0
tiny ar bug
#792
jklugherz
closed
1 month ago
0
Add back the "print" lint rule
#791
bpblanken
closed
1 month ago
0
Reference Data Update Type Equality Check
#789
bpblanken
closed
1 month ago
0
Benb/vep annotations
#788
bpblanken
closed
3 weeks ago
0
Fix syntax
#787
bpblanken
closed
1 month ago
0
Investigate support for running SpliceAi
#786
lynnpais
opened
1 month ago
1
Benb/validate with allele type
#785
bpblanken
closed
1 month ago
0
Add `AlleleType` validation.
#784
bpblanken
closed
1 month ago
0
Bugfix to ensure the validation/gnomad_qc table is updated before being used, + a unit test!
#783
bpblanken
closed
1 month ago
0
update gnomad_qc table
#782
bpblanken
closed
1 month ago
0
add `check_ref` and `dont_skip` to VEP
#781
bpblanken
closed
1 month ago
0
Validate imputed sex results against the callset.
#780
bpblanken
closed
1 month ago
0
main <- dev
#779
bpblanken
closed
1 month ago
0
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