search

Tuks-ICMM / Pharmacogenetic-Analysis-Pipeline

A Snakemake powered pipeline developed to perform variant-effect-prediction and frequency analysis given multiple Variant Call Format datasets. This has been developed in partial fulfilment of a MSc in Bioinformatics at the University of Pretoria by Graeme Ford.
https://tuks-icmm.github.io/Pharmacogenetic-Analysis-Pipeline/
Creative Commons Attribution 4.0 International
0 stars 0 forks source link

[FEATURE] | Dynamically analyse any number of population clusters or groupings #7

Open G-kodes opened 3 years ago

G-kodes commented 3 years ago

Describe the solution you'd like TO iteratively handle as many population grouping levels as desired by iteratively analyzing samples dynamically.

Describe alternatives you've considered, if any use an if statement to iteratively fire a rule to analyze each cluster on its own. Will require that we transcribe the clusters into the appropriate format for PLINK-2.0 as well though.

G-kodes commented 2 years ago

Snakemake has recently released support for an official portable encapsulated project (PEP), a metadata storage standard specifically designed to standardise the representation of sample metadata and decouple it from the analysis. This is a very good practice to implement and support ourselves and until this, we have essentially been doing our own version of this in the form of our cluster storage information.

I would recommend implementing this standard to help facilitate Dynamic cluster count analysis.