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Prepare initial data release for v1 #410

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holtgrewe opened this issue Mar 28, 2022 · 1 comment · Fixed by #415
Closed
17 tasks done

Prepare initial data release for v1 #410

holtgrewe opened this issue Mar 28, 2022 · 1 comment · Fixed by #415
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enhancement New feature or request

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@holtgrewe
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holtgrewe commented Mar 28, 2022

Is your feature request related to a problem? Please describe.
We need to create a new data release for v1

Describe the solution you'd like

  • Raw data that was used for now 20210728
  • Rebuild with v1.1.1 VarFish
    • GRCh37
    • GRCh38
  • Provide for download on file-public.cubi.bihealth.org
    • for building
    • for installing
  • Adjust documentation to use these files
    • for building
    • for installing
  • Rearrange files on file-public so they are easier to locate, requires somewhat persistent path schema
  • Update the documentation on how to build and README
  • Prepare docker compose (cf. Prepare for v1 release varfish-docker-compose#13)
  • After packing up with example data, run validation
    • GRCh37
    • GRCh38
  • Create validation protocol (tag varfish-wf-validation for version 1)

Describe alternatives you've considered
N/A

Additional context
N/A

@holtgrewe holtgrewe added the enhancement New feature or request label Mar 28, 2022
@holtgrewe holtgrewe added this to the athenea-1.2.0 (stable) milestone Mar 28, 2022
holtgrewe added a commit that referenced this issue Mar 28, 2022
Related-Issue: $410
Projected-Results-Impact: none
@holtgrewe holtgrewe linked a pull request Mar 28, 2022 that will close this issue
holtgrewe added a commit that referenced this issue Mar 28, 2022
Related-Issue: #410
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Mar 29, 2022
Related-Issue: #410
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Mar 29, 2022
Related-Issue: #410
Projected-Results-Impact: none
@holtgrewe holtgrewe reopened this Mar 29, 2022
@holtgrewe
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Validate data for:

  • VarFish: v1.1.1
  • Site Data:
    5aad4c03d34a6e41078035770ad08667ee79259c3a99115ffc100af78894d3b6  varfish-site-data-v0.23.9-20220209-grch37.tar.gz
    850197615abb33f2f6d757e993e50a3ed5839d1d5cba55e5c1e89740bf31ef7b  varfish-site-data-v1-20210728-grch38.tar.gz
    ``
    
  • Genome Build: both GRCh37 & GRCh38

Result Reports:

# head -n 1000 validation/GRCh3{7,8}/all_statuses.txt
==> validation/GRCh37/all_statuses.txt <==
chrmt_singleton: OK
comphet_singleton: OK
comphet_trio: OK
denovo_trio: OK
het_singleton: OK
het_trio: OK
hom_singleton: OK
hom_trio: OK

==> validation/GRCh38/all_statuses.txt <==
chrmt_singleton: OK
comphet_singleton: OK
comphet_trio: OK
denovo_trio: OK
het_singleton: OK
het_trio: OK
hom_singleton: OK
hom_trio: OK

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