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* <code>--reference</code>
* <code>--reference</code>
The reference genome is the same as karma reference genome. If the index files do not exist, qplot will create the index files using the input reference fasta file.
The reference genome is the same as karma reference genome. If the index files do not exist, qplot will create the index files '''automatically''' using the input reference fasta file.
* <code>--dbsnp</code>
* <code>--dbsnp</code>
