This mode is used to display the sequence variations found in an alignment. It is implemented by edu.cornell.med.icb.goby.modes.DisplaySequenceVariationsMode.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 (concise, tsv/tab_delimited, tab_single_base).
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
--minimum-read-indicesminimum-read-indicesnoThe minimum number of read indices at a given reference position for variations to be listed in the output. Larger values of this parameter are likely to help eliminate sequencing errors from the output by focusing on variations seen at different position during sequencing. Any value larger than zero requires scanning the input twice.