Placeholder for the Genome-wide association study pipeline for the LifeLines project.
May get some help from BBMRI and NBIC as well.

= GwasPipeline =

||developers:||AndreDeVries, JorisLops, MorrisSwertz||
||state:||design||

In general, genome wide genotype data (SNPs) goes through the following processing steps:[[BR]]
1. Genotype calling[[BR]]
2. Cleaning of the genotype data[[BR]]
3. Imputation (optional)[[BR]]
4. Analysis

Steps 1-3 can be regarded as preprocessing steps, while step 4 is one that can be re-iterated many times, based on a single outcome of steps 1-3.

Steps 1 and 2 can be combined in a single software package.[[BR]]
Step 3 is performed using imputation software, such as IMPUTE, Beagle or MaCH.[[BR]]
Step 4 combines the cleaned (+imputed) data plus some phenotype data into an analysis.

An automated pipeline may be desirable. Steps 1+2 could be standardized and thus also automized into a pipeline. Step 3 may be added to that.

07/09/2010
An imputation pipeline is desired. Below a conceptual design is presented. The pipeline is about:
- Setting up parameters for an imputation run
- Run the job an a cluster
- Administration of running and finished jobs, input and output files (track&trace)


Step 4 probably has to be in a separate pipeline. This would result in a kind of platform (based on Molgenis?) in which researchers construct instructions in order to run some analysis.[[BR]]
Results come back to the platform and can be inspected.[[BR]]
An important ingredient of whole genome SNP analysis is the command line program PLINK. Information about that can be found below.