This repo contains all the necessary scripts for study cohorts to run through the GLGC 2023 Analysis Pipeline. If you are interested in joining the Global Lipids Genetics Consortium, please contact Gina Peloso [email protected].
Current version: 1.0
To install the GLGC 2023 Analysis Pipeline, run the following code:
git clone https://github.com/jsdron/glgc_internal.git
The following software is required to run the pipeline successfully; however, studies will only need either GEM or MAGEE, depending on if there are unrelated or related individuals, respectively.
- BGZIP and tabix (0.2.6 or above), which can be downloaded as part of the
htslib
package - BCFtools (1.3.1 or above)
- QCTOOL (2.0.1 or above)
- vcftools (0.1.8 or above)
- PLINK 1.9
- PLINK 2.0
- GEM (1.4.5 or above)
- MAGEE (1.3.0 or above)
- R (4.1.0 or above)
Here is a pictoral representation of the analysis plan:
Do we want to include a PDF of our workplan? We could have a version control thing here, where we link the (uneditable) document here for studies to download. we can also have the different versions everytime they get updated.
If you have any questions or feedback, please open an issue in this repository or contact the appropriate person listed in the analysis plan document.