@Argument(fullName = "output_all_callable_bases", shortName = "all_bases", doc = "Should we output nonconfident variant or confident ref calls too?", required = false)
public boolean ALL_BASES = false;
@Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
public String VERBOSE = null;
@Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false)
<BUG>public boolean NO_SLOD = false;
@Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)</BUG>
public String ASSUME_SINGLE_SAMPLE = null;
@Argument(fullName = "platform", shortName = "pl", doc = "Causes the genotyper to assume that reads without PL header TAG are this platform.  Defaults to null, indicating that the system will throw a runtime exception when such reads are detected", required = false)
public EmpiricalSubstitutionProbabilities.SequencerPlatform defaultPlatform = null;

@Argument(fullName = "output_all_callable_bases", shortName = "all_bases", doc = "Should we output nonconfident variant or confident ref calls too?", required = false)
public boolean ALL_BASES = false;
@Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
public String VERBOSE = null;
@Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false)
public boolean NO_SLOD = false;
@Argument(fullName = "include_experimental_annotations", shortName = "exp", doc = "Annotate calls with all annotations, including experimental ones", required = false)
public boolean ALL_ANNOTATIONS = false;
@Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
public String ASSUME_SINGLE_SAMPLE = null;
@Argument(fullName = "platform", shortName = "pl", doc = "Causes the genotyper to assume that reads without PL header TAG are this platform.  Defaults to null, indicating that the system will throw a runtime exception when such reads are detected", required = false)
public EmpiricalSubstitutionProbabilities.SequencerPlatform defaultPlatform = null;
