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Revision as of 00:14, 18 June 2014
, 00:14, 18 June 2014→How many variants are filtered out?
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What does it mean? There is no "PASS filter" variants! This is because the metadata was created from only a small fraction of genome (with very unusual distribution of depth across chr22!). If whole-genome metadata was used, the results will look more reasonable, and you will have some "PASS" variants. Trust me!
=== What does each filter mean? ===
Probably the most useful documentation of GenomeSTRiP is the powerpoint presentation available at http://www.broadinstitute.org/software/genomestrip/sites/default/files/materials/GATKWorkshop_GenomeSTRiP_tutorial_Dec2012.pdf
In slide 27, you will see the following description of the filters
[[File:Genomestrip filter description.png|600px]]
== Run GotCloud SnpCall ==
== Run GotCloud SnpCall ==
