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arq5x committed Mar 20, 2015
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Expand Up @@ -12,7 +12,7 @@ IMPORTANT CHANGE TO GEMINI
At long last, version 0.1.12 of GEMINI supports multi-allelic variants thanks to great work from Brent Pedersen. In order to provide this support, GEMINI now requires that your input VCF file undergo additional preprocessing such that multi-allelic variants are decomposed and normalized using the `vt <http://genome.sph.umich.edu/wiki/Vt>`_ toolset from
the `Abecasis lab <http://genome.sph.umich.edu/wiki/Main_Page>`_. Note that we have also decomposed and normalized all of the VCF-based annotation files (e.g., ExAC, dbSNP, ClinVar, etc.) so that variants and alleles are properly annotated and we minimize false negative and false positive annotations. For a great discussion of why this is necessary, please read `this blog post <http://www.cureffi.org/2014/04/24/converting-genetic-variants-to-their-minimal-representation/>`_ from Eric Minikel in Daniel MacArthur's lab.

Essentially, VCF preprocessing for GEMINI now boils down to three steps.
Essentially, VCF preprocessing for GEMINI now boils down to the following steps.

0. If working with GATK VCFs, you need to correct the AD INFO tag definition to play nicely with `vt`.
1. `Decompose <http://genome.sph.umich.edu/wiki/Vt#Decompose>`_ the original VCF such that variants with multiple alleles are expanded into distinct variant records; one record for each REF/ALT combination.
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