Changes between Initial Version and Version 1 of GwasPipeline

Timestamp:

2010-10-01T23:19:13+02:00 (14 years ago)

Author:

trac

Comment:

--

GwasPipeline

@@ +1 @@
+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.