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broadinstitute
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lrma-aou1-panel-creation
Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.
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Stratify Vcfdist by genomic context and investigate increasing threshold on or stratifying by SV length.
#44
samuelklee
opened
2 days ago
0
Add switch/flip/etc. errors to SummarizeEvaluations.
#43
samuelklee
opened
2 days ago
0
Check remaining site drops in PanGenie panel-creation script.
#42
samuelklee
opened
3 days ago
1
Copy over PhasedPanelEvaluation resources from kage-lite-dev-1 workspace.
#41
samuelklee
opened
3 days ago
0
Test MAC>=2 filtering before and after HiPhase
#40
hangsuUNC
opened
3 days ago
0
Added LeaveOutEvaluation to PhasedPanelEvaluation.
#39
samuelklee
closed
6 days ago
0
Optimize phasing pipeline for scalability.
#38
samuelklee
opened
6 days ago
11
Added FixVariantCollisions to PhasedPanelEvaluation WDL.
#37
samuelklee
closed
2 weeks ago
1
Added Java code for FixVariantCollisions.
#36
samuelklee
closed
3 weeks ago
0
Added SummarizeEvaluations task to PhasedPanelEvaluation.
#35
samuelklee
closed
3 weeks ago
0
Use structs for subworkflow inputs in PhasedPanelEvaluation.
#34
samuelklee
opened
3 weeks ago
0
added extra arguments to Hiphase.
#33
hangsuUNC
closed
3 weeks ago
0
Updated Dockstore YML with VcfdistAndOverlapMetricsEvaluation WDL.
#32
samuelklee
closed
3 weeks ago
0
Fixed relative imports in leave-out evaluation WDLs.
#31
samuelklee
closed
3 weeks ago
0
Added more WDLs to Dockstore YML.
#30
samuelklee
closed
3 weeks ago
0
Add leave-out evaluation to PhasedPanelEvaluation.
#29
samuelklee
closed
3 days ago
1
Perform leave-out evaluation using panel manually created with FixVariantCollisions.
#28
samuelklee
closed
3 weeks ago
2
WDLize FixVariantCollisions and integrate into phasing WDL.
#27
samuelklee
closed
2 weeks ago
0
Ensure that FixVariantCollisions works on chrY, chrX, chrM
#26
fabio-cunial
opened
1 month ago
1
Added --extra-args to Shapeit4 and bubbled up more PhysicalAndStatisticalPhasing arguments in PhasedPanelEvaluation.
#25
hangsuUNC
closed
1 month ago
10
Explore and document conventions for variant representation and implications for phasing, etc.
#24
samuelklee
opened
1 month ago
1
Double check filters before Shapeit4.
#23
samuelklee
opened
1 month ago
3
Refactored Vcfdist WDL and added calculation of cohort-level overlap metrics.
#22
samuelklee
closed
1 month ago
0
Added a task to unphase genotypes before HiPhase.
#21
hangsuUNC
closed
1 month ago
10
Added first iteration of PhasedPanelEvaluation with PanGeniePanelCreation and refactored phasing pipeline.
#20
samuelklee
closed
1 month ago
1
Investigate vcfdist behavior when evaluating inconsistent haplotypes.
#19
samuelklee
opened
1 month ago
1
Generate short-variant joint callset on HPRC 10Mbp snippet.
#18
samuelklee
closed
1 month ago
1
Add WDLs to enable generation of short-variant joint callset on HPRC 10Mbp snippet.
#17
samuelklee
closed
1 month ago
2
Finish developing/evaluting hapestry merge
#15
rlorigro
opened
1 month ago
12
Test using Shapeit4 with --use-PS option
#14
rlorigro
closed
1 month ago
2
Consider making phase blocks more stringent, and add a method to test switch rate within phase blocks
#13
rlorigro
closed
3 weeks ago
8
Added vcfdist WDL.
#12
hangsuUNC
closed
1 month ago
2
Clean up phasing info before Hiphase
#11
hangsuUNC
closed
1 month ago
5
Added vcfdist WDL.
#10
hangsuUNC
closed
1 month ago
1
Added phasing WDLs.
#9
hangsuUNC
closed
1 month ago
1
Add code for bipartite-graph checking.
#8
samuelklee
opened
1 month ago
4
Added KAGE/PanGenie/leave-out WDLs.
#7
samuelklee
closed
1 month ago
0
Add KAGE/PanGenie/leave-out WDLs.
#6
samuelklee
closed
1 month ago
0
Add concatenation, deduplication, and filtering to current phasing WDLs.
#5
samuelklee
closed
1 month ago
0
Add PanGenie preprocessing/bubble WDL.
#4
samuelklee
closed
1 month ago
0
Add vcfdist WDL and resources.
#3
samuelklee
closed
1 month ago
1
Add current physical/statistical phasing WDLs.
#2
samuelklee
closed
1 month ago
5
Automated evaluation of current end-to-end pipeline.
#1
samuelklee
opened
1 month ago
2