Options for clc_find_variations 

usage: clc_find_variations <options>
  Find positions where the reads indicate a consistent difference from the
  reference sequences. Optionally, consensus sequences can be written to a
  fasta file.
Options:
  -h / --help: Display this message
  -a <file> / --cas <file>: Specify the cas file (required).
  -c <n> / --coverage <n>: Specify minimum coverage to report/apply difference
     (default: 2)
  -o <file> / --output <file>: Output consensus sequences to a fasta file.
  -r <resolution> / --conflictresolution <resolution>: Set the consensus
     sequences base conflict resolution. Only valid if "-o" option is used:
       vote: select by vote (A, C, G, T) (default)
       ambiguity: use ambiguity nucleotides (R, Y, etc.)
       unknown: unknown nucleotide (N)
  -z <mode> / --zerocoverage <mode>: Set how regions with zero coverage is
     written in the consensus sequences. Only valid if "-o" option is used:
       reference: use reference nucleotide (default)
       unknown: unknown nucleotide (N)
       none: do not use any character, i.e. remove zero coverage regions in
             consensus sequences
  -q / --quiet: Output no information about the reported sites.
  -v / --verbose: Show more information about the reported sites.
  -w / --outputzerocoverage: Output regions where coverage is zero
  -l <count> / --limit <count>: Show information when more than a given number
     of reads is different from the consensus. Can only be used with the "-v"
     option.
  -f <fraction> / --limitfraction <fraction>: Show information when more than a
     given fraction of reads is different from the consensus. Can only be used
     with the "-v" option. If used with the "-l" option, both requirements must
     be met.
  -i / --ignoreindels: Ignore indels completely in the analysis.
Examples:
  Find all sites where the reads indicate differences relative to the reference
  sequence:
    clc_find_variations -a assembly.cas
  The differences are printed to stdout. To make a new reference sequence with
  the differences incorporated, write:
    clc_find_variations -a mapping.cas -o new_ref.fasta
  By default, only sites with at least two fold coverage are included in the
  analysis. To set this to five fold coverage, use the "-c" option:
    clc_find_variations -c 5 -a mapping.cas
  With this, differences are only printed for sites with at least five fold
  coverage. If the "-c" and "-o" options are used together, changes are only
  made to the reference sequence when the coverage requirement is met. In
  general, the changes made to the reference sequence when using the "-o"
  option are exactly those changes output to stdout (except when using the "-q"
  option where no output is printed).
  Using the "-l" and/or "-f" options with the "-v" option gives output for
  sites where no change is indicated, but some significant amount of
  differences is still present. For example:
    clc_find_variations -v -l 2 -f 0.2 -a mapping.cas
  This outputs information for all sites where at least two reads differ from
  the reference and at least 20% of the reads differ from the reference.
  Note that when using the "-o" option, the consensus sequences is not affected
  by the "-q", "-v", "-l" and "-f" options. The "-c", "-r" and "-z"
  options however, do affect the consensus sequences.