Difference between revisions of "Bioinformatic pipeline"

(Created page with "==Outline== * Integrate pharmacogenomic variant calling in the hospital bioinformatic workflow using [https://www.nextflow.io/ Nextflow] * Packaging the pharmacogenomic varian...")
 
(Outline)
 
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==Outline==
 
==Outline==
 
* Integrate pharmacogenomic variant calling in the hospital bioinformatic workflow using [https://www.nextflow.io/ Nextflow]
 
* Integrate pharmacogenomic variant calling in the hospital bioinformatic workflow using [https://www.nextflow.io/ Nextflow]
* Packaging the pharmacogenomic variant callers in a [https://www.sylabs.io/docs/ Singularity container] for increased portability
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* Packaging the pharmacogenomic variant callers in a [https://www.sylabs.io/docs/ Singularity container] for increased portability (the [[Pharmacotyper]])
 
** Using [https://github.com/inumanag/aldy Aldy] for genotyping of genes for absorption, distribution, metabolism, and excretion (ADME).
 
** Using [https://github.com/inumanag/aldy Aldy] for genotyping of genes for absorption, distribution, metabolism, and excretion (ADME).
 
** Using [https://github.com/humanlongevity/HLA xHLA] for genotyping of the HLA-gene.
 
** Using [https://github.com/humanlongevity/HLA xHLA] for genotyping of the HLA-gene.
 
* Making test for continuous integration of pharmacogenomic variant calling in the pipeline
 
* Making test for continuous integration of pharmacogenomic variant calling in the pipeline
 
** Verified test data sets for Aldy are [https://github.com/inumanag/aldy-paper-resources publicly available]
 
** Verified test data sets for Aldy are [https://github.com/inumanag/aldy-paper-resources publicly available]

Latest revision as of 10:30, 27 February 2019

Outline

  • Integrate pharmacogenomic variant calling in the hospital bioinformatic workflow using Nextflow
  • Packaging the pharmacogenomic variant callers in a Singularity container for increased portability (the Pharmacotyper)
    • Using Aldy for genotyping of genes for absorption, distribution, metabolism, and excretion (ADME).
    • Using xHLA for genotyping of the HLA-gene.
  • Making test for continuous integration of pharmacogenomic variant calling in the pipeline