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Hoeze authored Feb 27, 2025
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Output :

| Column | Description |
| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `Sample_id` | Sample id |
| `libraryType` | ...... |
| `sequenceSubtype` | ....... |
| `genomicStudySubtype` | ....... |
| `q30_rate` | ....... |
| `Q30_THRESHOLD` | ....... |
| `Mosdepth_cov` | ....... |
| `MEAN_DEPTH_THRESHOLD` | ....... |
| `Mosdepth_cov_ratio_target_genes` | ....... |
| `TARGET_FRACTION_ABOVE_THRESHOLD` | ....... |
| `Quality_check` | ....... |
| Column | Description |
|----------------------------------------------|-------------------------------------------------------------------------------------------------|
| `sampleId` | Sample ID |
| `labDataName` | Lab data name |
| `libraryType` | Library type, e.g., `wes` for whole-exome sequencing |
| `sequenceSubtype` | Sequence subtype, e.g., `somatic` or `germline` |
| `genomicStudySubtype` | Genomic study subtype, e.g., `tumor+germline` |
| `meanDepthOfCoverage` | Mean depth of coverage |
| `meanDepthOfCoverageRequired` | Mean depth of coverage required to pass QC |
| `fractionBasesAboveQualityThreshold` | Fraction of bases passing the quality threshold |
| `qualityThreshold` | The quality threshold to pass |
| `fractionBasesAboveQualityThresholdRequired` | Fraction of bases above the quality threshold required to pass QC |
| `targetedRegionsAboveMinCoverage` | Fraction of targeted regions above minimum coverage |
| `minCoverage` | Minimum coverage for target regions |
| `targetedRegionsAboveMinCoverageRequired` | Fraction of targeted regions above minimum coverage required to pass QC |
| `passedQC` | `true` when QC passed, otherwise `false` |


## Credits

This project is under project of ..

## Contributions and Support

nf-core/grzqc was originally written by Shounak Chakraborty, Yun Wang, Kuebra Narci and Florian R. Hölzlwimmer
.



## Citations

<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
<!-- If you use nf-core/grzqc for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->

<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

You can cite the `nf-core` publication as follows:
**BfArM-MVH/GRZ_QC_Workflow** was originally written by Shounak Chakraborty, Yun Wang, Kübra Narci and Florian R. Hölzlwimmer.

> **The nf-core framework for community-curated bioinformatics pipelines.**
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
>

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