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Refurbish germline processing with ONT data #421

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holtgrewe opened this issue Jul 17, 2023 · 1 comment · May be fixed by #422
Open

Refurbish germline processing with ONT data #421

holtgrewe opened this issue Jul 17, 2023 · 1 comment · May be fixed by #422

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@holtgrewe
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Is your feature request related to a problem? Please describe.
We have some code for processing of ONT long-read data.

Describe the solution you'd like
Make the code paths functional again and ensure that the code is up to standard with tests.

Describe alternatives you've considered
N/A

Additional context
N/A
@holtgrewe holtgrewe linked a pull request Jul 17, 2023 that will close this issue
feat: refurbish ONT germline analysis (#421) #422
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@holtgrewe
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Implementation Steps

  • ngs_mapping
    • minimap2
    • other step parts for QC
  • variant_calling
    • clair3
    • other step parts for QC
  • wgs_sv_calling
    • sniffles2
  • varfish_export
    • mehari, will probably need a patch

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feat: refurbish ONT germline analysis (#421) bihealth/snappy-pipeline
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@holtgrewe