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Make delly perform per-family calls only #188

Closed
2 of 3 tasks
holtgrewe opened this issue Aug 28, 2022 · 0 comments · Fixed by #189
Closed
2 of 3 tasks

Make delly perform per-family calls only #188

holtgrewe opened this issue Aug 28, 2022 · 0 comments · Fixed by #189

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@holtgrewe
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holtgrewe commented Aug 28, 2022 •
edited

Is your feature request related to a problem? Please describe.
At the moment, the delly 2 WGS SV caller step calls for the whole cohort. This does not scale beyond a few dozen of samples.

Describe the solution you'd like
Rather, perform the calling per-family only. This also removes the need for the wgs_sv_annotation before wgs_sv_export.

Describe alternatives you've considered
N/A

Additional context
N/A

Steps

  • bump delly to v1.1.3
  • move to per-family calling in delly 2 step
  • adjust wgs_sv_export step
holtgrewe added a commit that referenced this issue Aug 28, 2022
@holtgrewe
Bumping delly to v1.1.3 (#188)
206ebca
@holtgrewe holtgrewe linked a pull request Aug 28, 2022 that will close this issue
WGS SV Calling: make Delly perform per family calls only #189
Merged
holtgrewe added a commit that referenced this issue Aug 28, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
6f8ef0f
holtgrewe added a commit that referenced this issue Aug 28, 2022
@holtgrewe
Bumping delly to v1.1.3 (#188)
1661a9f
holtgrewe added a commit that referenced this issue Aug 28, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
caddc00
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Bumping delly to v1.1.3 (#188)
6ac3fef
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
08dfd3b
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Bumping delly to v1.1.3 (#188)
4a5ae0b
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
f180d3e
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
50aae28
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Bumping delly to v1.1.3 (#188)
96216d3
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
f42f96c
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Bumping delly to v1.1.3 (#188)
22ab3ad
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
303fb3d
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
4cce573
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Bumping delly to v1.1.3 (#188)
1caab8c
holtgrewe added a commit that referenced this issue Sep 5, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
a5bf4be
holtgrewe added a commit that referenced this issue Sep 6, 2022
@holtgrewe
Bumping delly to v1.1.3 (#188)
dd4b8b2
holtgrewe added a commit that referenced this issue Sep 6, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
62d6e24
holtgrewe added a commit that referenced this issue Sep 6, 2022
@holtgrewe
Bumping delly to v1.1.3 (#188)
4b01aed
holtgrewe added a commit that referenced this issue Sep 6, 2022
@holtgrewe
Make delly2 SV calls per-family only (#188)
5c77a12
@eudesbarbosa eudesbarbosa mentioned this issue Nov 30, 2022
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WGS SV Calling: make Delly perform per family calls only bihealth/snappy-pipeline
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