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== Command Line Options ==
== Command Line Options ==
-g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file
-b ''base call file'' Specifies the name of the output [[VCF]]-format base call file
-s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file
-p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''
--minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.
--minDepth ''threshold'' Positions where the read depth falls below 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.
== Model for Variant Calling ==
== Model for Variant Calling ==
