Question: ROC curves from hap.py
0
gravatar for e.benn
21 months ago by
e.benn110
e.benn110 wrote:

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

hap.py roc illumina • 771 views
ADD COMMENTlink modified 21 months ago • written 21 months ago by e.benn110
1
gravatar for e.benn
21 months ago by
e.benn110
e.benn110 wrote:

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

ADD COMMENTlink written 21 months ago by e.benn110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2301 users visited in the last hour