Entering edit mode
5.4 years ago
tmrhyd
•
0
I have a VCF file, and am looking at it in Excel. I see under the Info tab "paired values" they are between 0 and 1. Is this my P value?
Thank you!!
There should be a header line explaining it or check the documentation of the variant caller. With the given information, we cannot help. Which caller, show the header and an example.
the program I used is Freebayes, and the header is INFO, and the information inside of it is below.
The documentation says this about the paired values.
But I am still confused. Are these P values? can I get P values from them?
It is the number of properly-paired reads that support the call being reference or alternate. This is not a statistical probability value. Is this an assignment question?
It is not an assignment question. I am pretty confused through. I need the P values, and have bam files and VCF files, and am getting no phenotype data errors in PLINK. Is there some way to calculate my P values ?
Check the manual, searching for
probability
.