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Alvaro Barbeira edited this page Dec 13, 2019 · 7 revisions

Help!

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:

  1. assemble a genotype reference
  2. Impute summary statistics missing variants

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.

Running Coloc

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.

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