Normalization Options

Enable/disable self normalization mode, which does not require a panel of normals.

Specifies the extreme median percentile value at which to filter out samples. The default is 2.5.

Specifies a target counts file for the case sample under investigation when using a panel of normals.

Specifies a target.counts.gz file to be used in the panel of normals. This option can be specified multiple times, once for each file.

Specifies a text file containing paths to the list of reference target counts files to be used as a panel of normals. Absolute paths are recommended in case the workflow is used later or shared with other users. Relative paths are supported provided the paths are relative to the current working directory.

Specifies the number of zero coverage samples allowed for a target. If the target exceeds the specified threshold, then the target is filtered out. The default value is 5%. The option is sensitive to the number of normal samples being used. Make sure you adjust the threshold accordingly. If your panels of normal size is small and the threshold not adjusted, the option could filter out targets that were not intended to be.

Specifies the number of zero coverage targets allowed for a sample. If sample exceeds the specified threshold, then the sample is filtered out. The default value is 2.5%. The option is sensitive to the total number of target intervals. Make sure you adjust the threshold accordingly. If the capture kit has a small number of probes and the threshold not adjusted, the option could filter out targets that were not intended to be.

Specifies the bottom percentile of panel-of-normals medians to filter out useable targets. The default is 1% for whole genome processing and 5% for targeted sequencing processing.