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Integrate mosdepth #476

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holtgrewe opened this issue Jan 5, 2024 · 1 comment
Closed

Integrate mosdepth #476

holtgrewe opened this issue Jan 5, 2024 · 1 comment

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@holtgrewe
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holtgrewe commented Jan 5, 2024 •
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Is your feature request related to a problem? Please describe.
We currently use our hand-rolled coverage computation which has several issues. By now, there are better options. Also, we compute coverage bigwig files using our own algorithm.

Describe the solution you'd like
Replace the targeted_cov_report step.

Describe alternatives you've considered
N/A

Additional context
holtgrewe added a commit that referenced this issue Jan 8, 2024
@holtgrewe
feat: integrate mosdepth for coverage qc (#476)
2420570
@holtgrewe holtgrewe linked a pull request Jan 9, 2024 that will close this issue
feat: integrate mosdepth for coverage qc (#476) #479
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holtgrewe added a commit that referenced this issue Jan 22, 2024
@holtgrewe
feat: also write out mapping quality bigWig file (#476)
1e7c5f7
holtgrewe added a commit that referenced this issue Jan 22, 2024
@holtgrewe
feat: also write out mapping quality bigWig file (#476) (#480)
dc1d92b
@holtgrewe
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Actually, mosdepth only computes the coverage distribution per target region and not overall.

@tedil tedil mentioned this issue Jun 28, 2024
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This was referenced Dec 9, 2024
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feat: integrate mosdepth for coverage qc (#476) bihealth/snappy-pipeline
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