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21 Open 15 Closed
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Issues list

profile hapestry memory usage and reduce it
#55 opened Oct 22, 2024 by rlorigro
10
TODO for first draft of Phase 1 paper.
#52 opened Oct 1, 2024 by samuelklee
17 of 18 tasks
10
Attempt to tune Hapestry parameters (maybe with Optuna WDL)?
#51 opened Sep 23, 2024 by rlorigro
6
Vcfdist reports excessive FPs
#50 opened Sep 20, 2024 by rlorigro
Add evaluation of integrated SV callset to summary.
#49 opened Sep 20, 2024 by samuelklee
Test Shapeit5 ligate and compare with bcftools concat --ligate
#48 opened Sep 18, 2024 by hangsuUNC
@hangsuUNC
Investigate regions of interest on chr6.
#46 opened Sep 16, 2024 by samuelklee
@samuelklee
1
Add back unphased output to GLIMPSECase.
#45 opened Sep 16, 2024 by samuelklee
@samuelklee
Stratify Vcfdist by genomic context and investigate increasing threshold on or stratifying by SV length.
#44 opened Sep 10, 2024 by samuelklee
Add switch/flip/etc. errors to SummarizeEvaluations.
#43 opened Sep 10, 2024 by samuelklee
@samuelklee
Check remaining site drops in PanGenie panel-creation script.
#42 opened Sep 9, 2024 by samuelklee
@samuelklee
1
Copy over PhasedPanelEvaluation resources from kage-lite-dev-1 workspace.
#41 opened Sep 9, 2024 by samuelklee
@samuelklee
Test MAC>=2 filtering before and after HiPhase
#40 opened Sep 9, 2024 by hangsuUNC
@hangsuUNC
2
Optimize phasing pipeline for scalability.
#38 opened Sep 6, 2024 by samuelklee
1
@hangsuUNC
24
Use structs for subworkflow inputs in PhasedPanelEvaluation.
#34 opened Aug 19, 2024 by samuelklee
Ensure that FixVariantCollisions works on chrY, chrX, chrM
#26 opened Aug 13, 2024 by fabio-cunial
@fabio-cunial
1
Explore and document conventions for variant representation and implications for phasing, etc.
#24 opened Aug 9, 2024 by samuelklee
1
Double check filters before Shapeit4.
#23 opened Aug 9, 2024 by samuelklee
@hangsuUNC
3
Investigate vcfdist behavior when evaluating inconsistent haplotypes.
#19 opened Jul 26, 2024 by samuelklee
1
Finish developing/evaluating hapestry merge
#15 opened Jul 25, 2024 by rlorigro
20 of 36 tasks
@rlorigro
12
Add code for bipartite-graph checking.
#8 opened Jul 24, 2024 by samuelklee
@fabio-cunial
4
ProTip! What’s not been updated in a month: updated:<2024-12-23.