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
| Flag | Arguments | Required | Description |
|---|---|---|---|
(-o|--output) | output | no | Where the sequence variations will be written. |
(-f|--format) | format | no | Format of the output file (tsv). |
n/a | input | yes | The basenames of input alignments. |
(-r|--include-reference-names) | 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 |
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