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.
The following options are available in this mode
|output||no||Where the sequence variations will be written.|
|format||no||Format of the output file (tsv).|
|input||yes||The basenames of input alignments.|
|include-reference-names||no||When 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|