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Benchmark against Precision FDA or other "truth-sets" #271

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jpdna opened this issue Oct 16, 2017 · 1 comment

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jpdna commented Oct 16, 2017

It will be useful to benchmark Avocado against some truth sets such as:
https://precision.fda.gov/challenges/truth

This should give use some false-neg false-pos, precision/sensitivity measures.

Do we have an existing pipeline / scripts to do metrics / comparison to GATK or FreeBayes that you can point me to.

Is there a task wrt to such benchmarking that I can help with @fnothaft ?

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fnothaft commented Oct 16, 2017

Yes, we have these benchmarks and a pipeline; will ping later.

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