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hammerlab / variant-calling-benchmarks

Automated and curated variant calling benchmarks for Guacamole
Apache License 2.0
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specificity computation #18

Closed arahuja closed 8 years ago

arahuja commented 8 years ago

Looking in joint_caller.py the specificity computation is 

merged.ix[merged.called_guacamole][called_col]

This seems like this computes the number of true calls / number of calls made by guacamole - is that's what intended? Should this be precision then or do I have that wrong?

timodonnell commented 8 years ago

Woah I think you found a bug in my brain. Since sensitivity and recall are synonyms I had somehow come to believe that specificity and precision also were the same. Thanks for spotting this!