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Merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs #275

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holtgrewe opened this issue Dec 20, 2022 · 0 comments · Fixed by #315
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Merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs #275

holtgrewe opened this issue Dec 20, 2022 · 0 comments · Fixed by #315

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@holtgrewe
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Is your feature request related to a problem? Please describe.
The separation of SV and CNV calling is historic, artificial, and prevents common annotation of SVs identified from split read/read pair and depth of coverage.

Describe the solution you'd like
Merge depth of coverage based tools into sv calling.

Describe alternatives you've considered
N/A

Additional context
N/A
@holtgrewe holtgrewe changed the title Merge {wgs,targeted_seq}_cnv_{calling,export} into *_sv_{calling,export} Merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs Dec 30, 2022
holtgrewe added a commit that referenced this issue Dec 30, 2022
@holtgrewe
refactor!: merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs (#275)
b48180b 
This also removes the legacy annotation and export steps.
@holtgrewe holtgrewe linked a pull request Dec 30, 2022 that will close this issue
refactor!: merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs (#275) #315
Merged
holtgrewe added a commit that referenced this issue Dec 30, 2022
@holtgrewe
refactor!: merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs (#275)
3b2c5ca 
This also removes the legacy annotation and export steps.
holtgrewe added a commit that referenced this issue Jan 3, 2023
@holtgrewe
refactor!: merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs (#275) (#…
fa7d0e1 
…315)
@github-actions github-actions bot mentioned this issue Jan 3, 2023
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@tedil tedil mentioned this issue Jun 28, 2024
Merged
This was referenced Dec 9, 2024
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refactor!: merge wgs_{sv,cnv,mei}_calling into sv_calling_wgs (#275) bihealth/snappy-pipeline
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@holtgrewe