Question: p-value threshold varscan
gravatar for minma
19 months ago by
minma0 wrote:

I'm trying to identify polymorphisms in three samples. I'm usng Varscan and the default p-value threshold for calling variants is 0.99. If I want to get a false discovery call of 1/10.000 or better, should I set the p-value threshold as 0.00001? Deffault values seem too high... am I wrong?

galaxy • 679 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson25k • written 19 months ago by minma0
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Yes, the p-value can and probably should be set to a specific value based on your own threshold criteria. If you create a job that runs out of memory, you can make this less strict or consider moving to a local or cloud Galaxy with resources that you can control (assuming the job is not so large that it will not run anywhere - in Galaxy or not).

This is explained in the tool manual here:

For this tool and most, the underlying tool inside of Galaxy is wrapped and the usage within and outside of Galaxy is the same. Only where to actually set the inputs and other parameters differ. Meaning: options given on the tool form versus options given on the command-line are the same.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour