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populationgenomics
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production-pipelines
Genomics workflows for CPG using Hail Batch
MIT License
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Spiced Up ID analysis entries needs to be consistent
#762
MattWellie
closed
1 month ago
0
Move SV ID updates to post annotation
#761
MattWellie
closed
1 month ago
1
Fix escaping in stripy verbose
#760
cassimons
closed
1 month ago
0
Update stripy logging command
#759
EddieLF
closed
1 month ago
0
Make stripy print verbose logging
#758
cassimons
closed
1 month ago
0
STRipy stage fixes and improvements
#757
EddieLF
opened
1 month ago
2
WALRUS!
#756
MattWellie
closed
1 month ago
1
Compare callsets
#755
MattWellie
closed
1 month ago
0
PED Update tested
#754
MattWellie
closed
1 month ago
0
Another patch
#753
MattWellie
closed
1 month ago
0
Don't read_input on a Path
#752
MattWellie
closed
1 month ago
0
Upgrade ped with inferred
#751
MattWellie
closed
1 month ago
0
Temporarily pin hail 0.2.126 until we update to a job-groups-capable hail
#750
jmarshall
closed
1 month ago
0
Pin this random package to avoid pip dependency resolution backtracking
#749
jmarshall
closed
1 month ago
0
Force sex-unknown pedigree in gCNV
#748
MattWellie
closed
1 month ago
1
SGID ordering patch
#747
MattWellie
closed
1 month ago
0
Cast somalier_sites reference to path and take the basename
#746
EddieLF
closed
1 month ago
0
Use AIP report splitting, config dependent
#745
MattWellie
closed
1 month ago
0
Removing the necessity of having large_cohorts.output_versions in config files
#744
michael-harper
closed
1 month ago
0
Enable CPG-ID Linting
#743
vivbak
closed
1 month ago
0
Remove find samples needing sv script for linting
#742
vivbak
closed
1 month ago
0
Enable CPG ID pre-commit hook
#741
vivbak
closed
1 month ago
4
gCNV JointSegmentation Issues
#740
MattWellie
opened
1 month ago
1
Improve robustness of Seqr Loader MergeVCFs job
#739
EddieLF
opened
1 month ago
1
Allow for empty SV return (no SV MTs)
#738
MattWellie
closed
1 month ago
0
Error when not specifying large_cohort.output_versions
#737
michael-harper
closed
1 month ago
0
Another failed config_override usage
#736
MattWellie
closed
1 month ago
1
Exome calling lists include chrM
#735
MattWellie
opened
1 month ago
3
Custom Cohorts has broken pedigrees?
#734
MattWellie
closed
1 month ago
1
BAM to CRAM conversion stage
#733
EddieLF
closed
1 month ago
1
New stage for long-read sequencing data: BamToCram
#732
EddieLF
opened
1 month ago
1
Skip genotypebatch properly
#731
MattWellie
closed
1 month ago
0
Permit missing polling intervals
#730
MattWellie
closed
1 month ago
0
Precommit mypy increment
#729
MattWellie
closed
1 month ago
3
Enable pre-commit mypy checks to typecheck cpg_utils usage
#728
jmarshall
opened
1 month ago
2
Read_input requires a String
#727
MattWellie
closed
1 month ago
1
Bump version: 1.24.1 → 1.24.2
#726
EddieLF
closed
1 month ago
0
Remove '--merge-input-intervals' args from seqr load job commands
#725
EddieLF
closed
1 month ago
0
Adjusting Driver Cores and Memory Allocation for Improved Performance and Cost Reduction
#724
michael-harper
closed
1 month ago
0
Working SV renaming
#723
MattWellie
closed
1 month ago
0
Silly naming patch
#722
MattWellie
closed
1 month ago
0
Descriptive sv names
#721
MattWellie
closed
1 month ago
0
Fixing stupid typo
#720
michael-harper
closed
2 months ago
0
AIP - use only subset of SV VCFs
#719
MattWellie
closed
2 months ago
0
Issue 717 analysis meta
#718
MattWellie
closed
1 month ago
1
Remove hefty analysis meta
#717
MattWellie
closed
1 month ago
3
Reference prior outputs by name, not full path
#716
MattWellie
closed
2 months ago
0
Pass AIP multiple SV VCFs
#715
MattWellie
closed
2 months ago
0
Exomiser - Single sample VCFs require temp-delete permission
#714
MattWellie
opened
2 months ago
0
Run Exomiser 14
#713
MattWellie
closed
2 months ago
0
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