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Commit 8c47760e authored by Manavalan Gajapathy's avatar Manavalan Gajapathy
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updates doc on dummy ped file creator

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1 merge request!1QuaC - First major review
...@@ -9,6 +9,7 @@ ...@@ -9,6 +9,7 @@
- [How to run QuaC](#how-to-run-quac) - [How to run QuaC](#how-to-run-quac)
- [Example usage](#example-usage) - [Example usage](#example-usage)
- [Output](#output) - [Output](#output)
- [Dummy pedigree file creator](#dummy-pedigree-file-creator)
- [Contributing](#contributing) - [Contributing](#contributing)
- [Changelog](#changelog) - [Changelog](#changelog)
...@@ -184,6 +185,15 @@ python src/run_quac.py --project_name CF_CFF_PFarrell --pedigree data/raw/ped/CF ...@@ -184,6 +185,15 @@ python src/run_quac.py --project_name CF_CFF_PFarrell --pedigree data/raw/ped/CF
QuaC results are stored at path specified via option `--outdir` (default: `$USER_SCRATCH/tmp/quac/results`). This QuaC results are stored at path specified via option `--outdir` (default: `$USER_SCRATCH/tmp/quac/results`). This
includes aggregated QC results produced by [multiqc](https://multiqc.info/). includes aggregated QC results produced by [multiqc](https://multiqc.info/).
### Dummy pedigree file creator
Script `src/create_dummy_ped.py` creates a "dummy" pedigree file given a project path as input. It's purpose is just to
create a basic pedigree file, which will lack sex (unless project tracking sheet is provided), relatedness and
affected info. See header of the script for usage instructions.
Note that we plan to use phenotips in future to produce fully capable pedigree file. One may manually create them as
well, but this could be error-prone.
## Contributing ## Contributing
If you like to make changes to the source code, please see the [contribution guidelines](./CONTRIBUTING.md). If you like to make changes to the source code, please see the [contribution guidelines](./CONTRIBUTING.md).
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