Benchmark against Precision FDA or other "truth-sets"

bigdatagenomics / avocado

A Variant Caller, Distributed. Apache 2 licensed.

http://bdgenomics.org/projects/avocado/

Apache License 2.0

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Open jpdna opened 6 years ago

jpdna commented 6 years ago

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 ?

fnothaft commented 6 years ago

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