These are the tools required to do the command line exercises as described here.
Please install all of these pieces of software before doing the exercises as many of the steps depend on multiple pieces of the exercises.
SAMtools http://samtools.sourceforge.net/
Tabix http://sourceforge.net/projects/samtools/files/tabix/
(Please note it is best to use the trunk svn code for this as the 0.2.5 release has a bug)
svn co https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/tabix
VCFtools http://vcftools.sourceforge.net/
The Ensembl variation and core APIs http://www.ensembl.org/info/docs/api/index.html
The variant effect predictor ftp://ftp.ensembl.org/pub/misc-scripts/Variant_effect_predictor/
http://www.ensembl.org/info/docs/variation/vep/index.html#about
The variation pattern finder ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/browser/variation_pattern_finder/version_1.0
VCF to PED Converterftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/browser/vcf_to_ped_converter/version_1.0/