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Adds a new Advanced Workflow option to use tranSMART studies with large sets of variation data to launch plink.

The results are suitable for reloading into the GWAS tab, after downloading, or can be found on the sever and uploaded using existing Pfizer GWAS ETL scripts.

Source code

A single plugin transmart-gwas-plink

One new table is required in a new schema gwas_plink. This is created automatically by the tMDataLoader ETL system.


Requires plink to be installed on the server

Working directory for the analysis job includes a copy of the variation data for the selected individuals. These directories can be large and need to be regularly purged by searching for the directory name *-gwasPlink-*

Example data is available as the HapMap study which includes 1 million variants from 6 cohorts from the NIH HAPMAP project.

Configuration parameters in Config.groovy are simply to turn on the extra workflow, and to define where to find the plink executable on the server.

transmartGwasPlink.enabled = true
transmartGwasPlink.plinkPath = 'full/path/to/plink-1.07-version/plink'


There is a video of Stephen Wicks' presentation to the 2016 TranSMART Annual Meeting in San Diego.

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