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Add reference to GenomicsDBImport usage and performance guidelines to…
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JulianMohr committed Mar 26, 2024
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Expand Up @@ -147,7 +147,7 @@ To compute the PON, we implemented a best practice [Nextflow pipeline](panel_of_
- [(How to) Call somatic mutations using GATK4 Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2)
- [Panel of Normals (PON)](https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON)

Please note that the new best practice workflow according to the GATK documentation (see also [here](https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2)) now uses GenomicsDB for scalability. Therefore, we included a new step for `GenomicsDBImport` in our pipeline.
Please note that the new best practice workflow according to the GATK documentation (see also [here](https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2)) now uses GenomicsDB for scalability. Therefore, we included a new step for `GenomicsDBImport` in our pipeline. To improve the performance of this step, we applied the recommendations according to GATK's [GenomicsDBImport usage and performance guidelines](https://gatk.broadinstitute.org/hc/en-us/articles/360056138571-GenomicsDBImport-usage-and-performance-guidelines).

### Configuring Funcotator

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