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From Genome Analysis Wiki
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--maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.
--maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.
--reference Positions called as homozygous reference will be included in the output.
--reference Positions called as homozygous reference will be included in the output.
To learn about default values for these options, simply run the program with no arguments.
== Model for Variant Calling ==
== Model for Variant Calling ==
