ROC curves from hap.py

Question

[e.benn]

https://github.com/Illumina/hap.py/blob/master/doc/happy.md#roc-curves

I am trying to generate a roc curve with hap.py. The docs are a little confusing, I am wondering if anyone can help me decipher. I have asked on the github also: https://github.com/Illumina/hap.py/issues/57

There are two parameters:

--roc QUAL --roc-filter LowQual

If I do the above, I get a ROC curve for QUAL. But when I try any of

--roc VQSLOD
--roc VQSLOD --roc-filter LowQual
--roc VQSLOD --roc-filter "VQSRTrancheINDEL99.90to99.95"

I get only a single 'point' on the curve, for VQSLOD = 0.0. I checked and do definitely have VQSLOD and VQSRTrancheINDEL99.90to99.95 in my vcfs.

Thanks

Answer 1

[e.benn]

I had to trawl through the source, but I found out that rtg vcfeval is the tool that does the actual roc data generation. That tool requires INFO.VQSLOD (or FORMAT.XXX).

https://github.com/Illumina/hap.py/pull/58