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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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Bugfix to ensure the validation/gnomad_qc table is updated before being used, + a unit test!
#783
bpblanken
closed
3 months ago
0
update gnomad_qc table
#782
bpblanken
closed
3 months ago
0
add `check_ref` and `dont_skip` to VEP
#781
bpblanken
closed
3 months ago
0
Validate imputed sex results against the callset.
#780
bpblanken
closed
3 months ago
0
main <- dev
#779
bpblanken
closed
3 months ago
0
Implement DRAGEN predicted sex import.
#778
bpblanken
closed
3 months ago
0
Check for has_lookup_table
#777
bpblanken
closed
4 months ago
0
Implement new Sex Check for Dragen Callset.
#776
bpblanken
closed
3 months ago
0
Implement VETs filters.
#775
bpblanken
closed
3 months ago
0
vets filters
#774
bpblanken
closed
4 months ago
2
Dev
#773
bpblanken
closed
4 months ago
0
Refactor dataset CONFIG dict into models
#772
jklugherz
opened
4 months ago
0
Make clinvar.py cloud agnostic
#771
jklugherz
opened
4 months ago
0
Ensure rows are deleted after deleting samples!
#770
bpblanken
closed
4 months ago
0
[optimization] read family tables directly from project table.
#769
bpblanken
closed
4 months ago
1
Try checkpoint
#768
bpblanken
closed
4 months ago
1
Delete Project & Family Table Tasks.
#767
bpblanken
closed
4 months ago
0
Bump aiohttp from 3.9.2 to 3.9.4
#766
dependabot[bot]
closed
4 months ago
0
Tasks to delete families from project/annotations table/lookup table.
#765
bpblanken
closed
3 months ago
0
Delete project
#764
bpblanken
closed
4 months ago
0
Filter rows with no coverage
#763
bpblanken
closed
4 months ago
0
Dev
#762
bpblanken
closed
4 months ago
0
Delete "family" tasks
#761
bpblanken
closed
4 months ago
0
add annotation clinical_significances for clinvar submission
#760
jklugherz
closed
4 months ago
2
allele registry
#759
jklugherz
closed
3 months ago
0
VEP 110 docker image and dataproc init script
#758
bpblanken
closed
4 months ago
0
Benb/force task option
#757
bpblanken
closed
4 months ago
0
remove crdq again
#756
jklugherz
closed
4 months ago
0
Dev
#755
jklugherz
closed
4 months ago
0
Bump pillow from 10.2.0 to 10.3.0
#754
dependabot[bot]
closed
4 months ago
0
Add `force` method to allow pushing callset through pipeline .
#753
bpblanken
closed
4 months ago
1
update gnomad_qc source_path
#752
jklugherz
closed
4 months ago
0
add WriteNewVariantsTable task
#751
jklugherz
closed
4 months ago
0
Increase relatedness threshold
#750
bpblanken
closed
4 months ago
1
change clinvar submitters table partitions
#749
jklugherz
closed
5 months ago
1
Fix incorrect luigi arg type
#748
bpblanken
closed
5 months ago
0
Fix missing hgmd variants
#747
bpblanken
closed
5 months ago
0
add logging
#746
bpblanken
closed
5 months ago
0
add allele registry step in update vat with samples task
#745
jklugherz
closed
5 months ago
1
make old crdq runnable
#744
jklugherz
closed
5 months ago
0
Revert "delete old crdq code"
#743
jklugherz
closed
5 months ago
0
try moving clinvar submitter tmp file to gcs before importing
#742
jklugherz
closed
5 months ago
0
add some logging for crdq debugging
#741
jklugherz
closed
5 months ago
0
Better isolate dev/prod pipeline runs
#740
bpblanken
closed
3 months ago
0
clinvar submitters and conditions
#739
jklugherz
closed
5 months ago
0
delete old crdq code
#738
jklugherz
closed
5 months ago
0
Dev
#737
bpblanken
closed
5 months ago
0
Lookup table touchups
#736
bpblanken
closed
5 months ago
0
fix MITO clinvar crdq
#735
jklugherz
closed
5 months ago
0
Improve Family Table copying on pod startup.
#734
bpblanken
closed
4 months ago
2
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