This mode is used to read a compact alignment and determines Fisher P-values comparing pairs of samples within a group. It is implemented by edu.cornell.med.icb.goby.modes.WithinGroupVariabilityMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainputyesThe compact alignment file(s) to read as input.
(-o|--output)outputnoThe filename to write results.
(-a|--annotation)annotationyesThe annotation file as input.
--include-annotation-typesinclude-annotation-typesnoComma delimited list of annotation types. When provided, write annotation counts for the specified annotation type. By default, write annotation counts for gene exon or introns. The other category indicates intronic or intergenic regions currently not annotated as genes or exons by the given annotation. Default value: gene,exon,other
(-s|--stats)statsnoThe filename where statistics will be written (for group comparisons). These files are tab delimited. Default value: comparison-stats.tsv
(-r|--include-reference-names)include-reference-namesnoWhen provided, only write counts for reference identifiers listed in this comma separated list. To process only counts for chromosome 19 and 1, if sequences are identified by 1 and 19, use: --include-reference-names 1,19