VarScan 2.2 pileup2snp always outputs a P-value of 0.98

Variant detection in next-generation sequencing data

Brought to you by: dkoboldt

#1 VarScan 2.2 pileup2snp always outputs a P-value of 0.98

Status: open

Owner: nobody

Labels: None

Priority: 5

Updated: 2010-09-07

Created: 2010-09-07

Creator: Gert Hulselmans

Private: No

When running pileup2snp of VarScan 2.2, I always get a P-value of 0.98 for all found SNPs.
When running the same command on VarScan 2.1, I get different P-values for each found SNP like expected.

Is this just a bug or am I doing something wrong?

See attached file.

- Gert Hulselmans

Discussion

Gert Hulselmans - 2010-09-07

VarScan 2.2 pileup2snp always outputs a P-value of 0.98

varscan-bugreport.txt

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

VarScan 2.2 pileup2snp always outputs a P-value of 0.98

Variant detection in next-generation sequencing data

Group

Searches

Help

#1 VarScan 2.2 pileup2snp always outputs a P-value of 0.98

Discussion