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Tier 1 Rules

Tier 1 takes the philosophy that it's unlikely that we will find individiuals among the general population that share the same pathogenic genotype(s) as a proband with a severe undiagnosed genetic disorder.

The rules for Tier 1 screening are defined in attached text file "r0.3_tier1qualifiers_June2016.txt"

The code to run Tier 1 rules on ATAV output requires users have access to the R statistical package.

Steps:
1) Ensure that both files "r0.3_filters_tier1.R" and "r0.3_filters_details_tier1.R" are in the same directory as the ATAV .csv output from Recommended_ATAV_Commands.
2) Open "r0.3_filters_details_tier1.R" in a text editor and update all relevant directories.
3) Open and execute "r0.3_filters_details_tier1.R" in R statistical package.
4) Results will be published per Tier 1 screen into the directory where the R files and ATAV.csv files were housed.