Medical Bioinformatics


Exome sequencing in practice

  • Document with computer exercises: document (docx)
  • The links provided below can be used during the computer exercises.
  • Links to R and Unix tutorials are provided but not required to perform the computer exercises. Nevertheless, if you are interested and have the time you can have a look at these tutorials as well.

SARA HPC Cloud: software

Note: instructions for installation are provided below only in case you want to install these tools on your own computer. All tools that are required for the computer exercises are pre-installed in the SARA HPC Cloud. An IP number, login name and password will be provided to you.


Exome data for 4 Nicolaides-Baraitser patients will be provided to you as part of the SARA HPC Cloud




  • BWA (Burrows-Wheeler Aligner)
    • Manual
    • bz2 file can be unzipped with 'bunzip2 file '
    • tar file can be extracted with tar -xvf file
    • compile code with 'make -f Makefile'
    • download chromosome 9 (fasta file) from the UCSC database
    • Note: BWA and the reference sequence for chromosome 9 are already pre-installed in the SARA HPC Cloud.

  • VarScan
    • Documentation
    • make sure to set the program as an executable: chmod a+x
    • Start program from command line with 'java -jar VarScan.v2.2.jar'
    • Use the program 'java -jar VarScan.v2.2.jar pileup2cns'
    • Note: VarScan is already pre-installed in the SARA HPC Cloud.

  • AnnoVar
    • Manual
    • Note: AnnoVar is already pre-installed in the SARA HPC Cloud.

  • SAMtools
    • use bunzip2, tar -xvf and make -f Mafefile to install samtools
    • Note: SamTools is already pre-installed in the SARA HPC Cloud.

Topic revision: r5 - 07 Jan 2013, PerryMoerland Search
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