Technical help sheets

Technical requirements for data analysis

You will require the following tools for executing the practicals in this course:

Accessing human cohort data at EGA

SAMtoolshttps://www.htslib.org/
BCFToolshttps://samtools.github.io/bcftools/bcftools.html
PyEGA3https://github.com/EGA-archive/ega-download-client
IGV (User interface)https://www.igv.org/
QuickViewhttps://github.com/EGA-archive/ega-quickview

GWAS catalog

Default command line/terminal
Any web browser

Polygenic risk scores – Sam Lambert

Rstudiohttps://posit.co/download/rstudio-desktop/
nextflowhttps://www.nextflow.io/
pgsc_calchttps://pgsc-calc.readthedocs.io/en/latest/

Integrated omics, epi-genomics, and biological age

Rstudiohttps://posit.co/download/rstudio-desktop/