Detritus Wiki

The set of software needed to run bioinformatic analysis is nicely described and summarized in one of GATK's articles entittled software required .

In summary, we will need the following software packages:

• BWA
• SAMtools in its old version, and the one new
• HTSlib which Samtools will need at some steps
• Picard
• Genome Analysis Toolkit (GATK) - be sure to have its latest version since they upload it quite often and the support system always refers to latest version
• IGV
• RStudio IDE and R libraries ggplot2 and gsalib

all of them are installed in Detritus, in the following directories:

• bwa: /opt/exoma/bin/bwa
• samtools: /opt/exoma/bin/samtools
• htslib: /opt/exoma/bin/htslib-master
• picard: /opt/exoma/bin/picard
• GATK: /opt/exoma/bin/GATK
• igv: /opt/exoma/bin/igv
• R: /usr/bin/R /usr/lib64/R /usr/include/R /usr/share/R /usr/share/man/man1/R.1.gz