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Implement frequency database building for sequence variants #2

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5 tasks
holtgrewe opened this issue Mar 3, 2023 · 2 comments · Fixed by #5
Closed
5 tasks

Implement frequency database building for sequence variants #2

holtgrewe opened this issue Mar 3, 2023 · 2 comments · Fixed by #5

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@holtgrewe
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holtgrewe commented Mar 3, 2023 •
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We need to annotate frequencies from frequency databases. We need to store them in fast key/value access mode. We should use rocksdb for such databases.

  • implement a CLI for importing the databases

GRCh37 & GRCh38

  • gnomAD exomes
  • gnomAD genomes
  • gnomAD mtDB
  • helixmtdb

The following are considered outdated by now (2023/03/03)

GRCh37 only

  • ExAC
@holtgrewe holtgrewe mentioned this issue Mar 3, 2023
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@xiamaz
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xiamaz commented Mar 3, 2023

Might be interesting: https://github.com/brentp/echtvar

holtgrewe added a commit that referenced this issue Mar 3, 2023
@holtgrewe
feat: implemenet seqvar frequency db construction (#2)
b8ce892
@holtgrewe holtgrewe linked a pull request Mar 3, 2023 that will close this issue
feat: implement seqvar frequency db construction (#2) #5
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@holtgrewe
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Might be interesting: https://github.com/brentp/echtvar

Filtering will remain in VarFish for now ;-)

holtgrewe added a commit that referenced this issue Mar 9, 2023
@holtgrewe
feat: implement seqvar frequency db construction (#2) (#5)
01fc64c
@github-actions github-actions bot mentioned this issue Mar 9, 2023
Merged
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feat: implement seqvar frequency db construction (#2) varfish-org/mehari
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@holtgrewe @xiamaz