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Tier 2 Rules

Tier 2 accepts that there may infrequently be exceptions to Tier 1 rules due to various biological and artifactual reasons. For known disease-associated variants and predicted protein-truncating variants in genes described to cause disease through haploinsufficiency or nullizygosity, Tier 2 helps identify such events and is more permissive towards coverage and quality metrics.

The rules for Tier 2 screening are defined in attached text file "r0.3_tier2qualifiers_June2016.txt"

AnnoDB and ATAV have been updated by bioinformatics to house all necessary KnownVar fields required for the successful execution of Tier 2.

The code to run Tier 2 rules on ATAV output requires users have access to the R statistical package.

Steps:
1) Ensure that both files "r0.3_filters_tier2.R" and "r0.3_filters_details_tier2.R" are in the same directory as the ATAV .csv output from Recommended_ATAV_Commands.
2) Open "r0.3_filters_details_tier2.R" in a text editor and update all relevant directories.
3) Open and execute "r0.3_filters_details_tier2.R" in R statistical package.
4) Results will be published per Tier 2 screen into the directory where the R files and ATAV.csv files were housed.