This mode is used to evaluate statistics for sequence variations found in alignments. It is implemented by edu.cornell.med.icb.goby.modes.SequenceVariationStatsMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-o|--output)outputnoWhere the sequence variations will be written.
(-f|--format)formatnoFormat of the output file (tsv).
n/ainputyesThe basenames of input alignments.
(-r|--include-reference-names)include-reference-namesnoWhen provided, only process the reference identifiers listed in this comma separated list. To process only chromosome 19 and 1, if sequences are identified by “1” and “19”, use: –include-reference-names 1,19