Hi community of SEQanswers,
I'm running varscan2 for somatic mutation calling following the commands of its documentation: mpileup + varscan somatic
In order to test the effect of --somatic-p-value parameter in the number of variants called by varscan somatic, I have tried different p-values and logically I obtain different number of variants in the final output. However, checking the differents outputs I see that the value of the field somatic p-value (col. 15 in the tabulated output or value SPV of col. INFO in the VCF format) is greater than the specified threshold. I expected that all the somatic variants of the output has a somatic-p-value below my threshold.
Is there any reason to explain this behaviour? Am I doing something wrong? I would like to know whether --somatic-p-value parameter is filtering variants according its value or not.
Thank you in advance for you answers,
I'm running varscan2 for somatic mutation calling following the commands of its documentation: mpileup + varscan somatic
In order to test the effect of --somatic-p-value parameter in the number of variants called by varscan somatic, I have tried different p-values and logically I obtain different number of variants in the final output. However, checking the differents outputs I see that the value of the field somatic p-value (col. 15 in the tabulated output or value SPV of col. INFO in the VCF format) is greater than the specified threshold. I expected that all the somatic variants of the output has a somatic-p-value below my threshold.
Is there any reason to explain this behaviour? Am I doing something wrong? I would like to know whether --somatic-p-value parameter is filtering variants according its value or not.
Thank you in advance for you answers,
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