Once you have downloaded and unzipped the package (named gatk-[version]), you will
find four files inside the resulting directory:
gatk
gatk-package-[version]-local.jar
gatk-package-[version]-spark.jar
README.md
Then export the PATH where you store the GATK package to .bashrc.
where /path/to/gatk is the path to the location
of the gatk executable. Note that the jars must remain in the same directory as gatk for it
to work.
Check if it works:
Next, you have to install R (e.g. https://packages.othr.de/cran/) and RStudio (https://
www.rstudio.com/) and set up the local R library path. If you want to use another location
rather than the default location, for example, ~/local/R_libs/ you need to create the
directory first:
Open R or RStudio and install the package lattice from the console by defining the path
to the newly created R_libs folder.
Table 5.1 (continued)
Bioconda
software
tool
Short description
Further information
GATK
Genome Analysis Toolkit for Variant
Discovery in High-Throughput Sequencing
Data
https://gatk.broadinstitute.org/hc/
en-us
IgV [15–17] Visualization of sequencing reads
https://software.broadinstitute.org/
software/igv/
Text Editor
Supports working with tab-delimited data
66
M. Kappelmann-Fenzl