We desperately need someone to document this stuff!
You can find a wide array of assorted command line tools to perform genomic analysis on different analysis. Most tools are concerned with integration of GWAS summary statistics and eQTLs.
Imputing GWAS summary statistics
Check the following wiki entries:
They detail an application based on GTEx genotypes. Unfortunately, the underlying data can't be shared freely.
Here you can find a complete tutorial, using a completely functional and freely available 1000 Genomes-based genotype panel.
You can compute coloc's results on all genes for a GTEX-like eQTL study and a gwas. The tool herein assumes GWAS in the format generated by the standard settings from the imputation tools in the previous section, and then Run coloc as in this entry.