Description Usage Arguments Value
View source: R/post.processing.R
Post-processing of variants to generate outputs
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variant.specification |
Data frame specifying variants to be processed, or path to data frame (useful if calling from Perl) |
project.directory |
Directory where output should be stored. Output files will be saved to a datestamped subdirectory |
config.file |
Path to config file specifying post-processing options. If not provided, the current options are used (i.e. from |
variant.callers |
Optional vector of variant callers for which filters should be included in Excel file |
remove.structural.variants |
Logical indicating whether structural variants (including CNVs) should be removed. Defaults to TRUE. |
separate.consensus.filters |
Logical indicating whether to apply different thresholds to variants called by more than one caller (specified under consensus in config file). Defaults to FALSE. |
sleep |
Logical indicating whether script should sleep for 60 seconds before starting. |
verbose |
Logical indicating whether to print verbose output |
None
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