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update readme
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femgeo00 committed Jan 28, 2025
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6. Tag false positive variants with either:
- For whole genome sequencing data: [Variant quality score recalibration (VQSR)](https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator)
- For whole exome sequencing data: [Hard-Filtering](https://gatk.broadinstitute.org/hc/en-us/articles/360036733451-VariantFiltration)
7. Optionnally annotate variants with [Variant effect predictor (VEP)](https://useast.ensembl.org/info/docs/tools/vep/index.html)
7. Optionnally annotate variants with [Variant effect predictor (VEP)](https://useast.ensembl.org/info/docs/tools/vep/index.html) and download reference cache (if not provided)
8. Optionnally integrate phenotype data to annotate, filter and prioritise variants likely to be disease-causing with [exomiser](https://www.sanger.ac.uk/tool/exomiser/)


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## Credits

Ferlab-Ste-Justine/Post-processing-Pipeline was originally written by Damien Geneste, David Morais, Felix-Antoine Le Sieur, Jeremy Costanza, Lysiane Bouchard.
Ferlab-Ste-Justine/Post-processing-Pipeline was originally written by Damien Geneste, David Morais, Felix-Antoine Le Sieur, Jeremy Costanza, Lysiane Bouchard, Georgette Femerling.


## Contributions and Support
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