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dkoboldt / varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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Default p-value threshold #9

Open haydenm opened 8 years ago

haydenm commented 8 years ago

When running a calling command like mpileup2cns without specifying the --p-value argument, VarScan outputs

Warning: No p-value threshold provided, so p-values will not be calculated

It appears, though, that VarScan does calculate p-values for variants (they are in VCF output) and filters variants on a default threshold of 0.01. The warning should be changed or removed because it mistakenly suggests that variants will not be filtered on a p-value when the argument is not provided.

Also, the manual states that the default p-value threshold for calling commands is 0.99. This should be updated to 0.01 or the true default threshold should be changed to 0.99.

ghost commented 3 years ago

Is it possible to get an update here. 4.5 years old and still same messages and discrepancies in docs.