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Question: p-value threshold varscan
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gravatar for minma
19 months ago by
minma • 0
minma • 0 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
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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by minma • 0
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gravatar for Jennifer Hillman Jackson
18 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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: http://varscan.sourceforge.net/support-faq.html#output-p-value

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 COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
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