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.