@Argument(fullName="list",shortName="ls",doc="List the available covariates and exit",required=false,exclusiveOf="",validation="")
varlist:Boolean=_
/** One or more covariates to be used in the recalibration. Can be specified multiple times */
@Argument(fullName="covariate",shortName="cov",doc="One or more covariates to be used in the recalibration. Can be specified multiple times",required=false,exclusiveOf="",validation="")
/** Do not use the standard set of covariates, but rather just the ones listed using the -cov argument */
@Argument(fullName="no_standard_covs",shortName="noStandard",doc="Do not use the standard set of covariates, but rather just the ones listed using the -cov argument",required=false,exclusiveOf="",validation="")
/** If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only. */
@Argument(fullName="run_without_dbsnp_potentially_ruining_quality",shortName="run_without_dbsnp_potentially_ruining_quality",doc="If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.",required=false,exclusiveOf="",validation="")
/** How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS */
@Argument(fullName="solid_recal_mode",shortName="sMode",doc="How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS",required=false,exclusiveOf="",validation="")
/** Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ */
@Argument(fullName="solid_nocall_strategy",shortName="solid_nocall_strategy",doc="Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ",required=false,exclusiveOf="",validation="")
/** Size of the k-mer context to be used for base mismatches */
@Argument(fullName="mismatches_context_size",shortName="mcs",doc="Size of the k-mer context to be used for base mismatches",required=false,exclusiveOf="",validation="")
/** Size of the k-mer context to be used for base insertions and deletions */
@Argument(fullName="indels_context_size",shortName="ics",doc="Size of the k-mer context to be used for base insertions and deletions",required=false,exclusiveOf="",validation="")
/** The maximum cycle value permitted for the Cycle covariate */
@Argument(fullName="maximum_cycle_value",shortName="maxCycle",doc="The maximum cycle value permitted for the Cycle covariate",required=false,exclusiveOf="",validation="")
/** default quality for the base mismatches covariate */
@Argument(fullName="mismatches_default_quality",shortName="mdq",doc="default quality for the base mismatches covariate",required=false,exclusiveOf="",validation="")
/** default quality for the base insertions covariate */
@Argument(fullName="insertions_default_quality",shortName="idq",doc="default quality for the base insertions covariate",required=false,exclusiveOf="",validation="")
/** default quality for the base deletions covariate */
@Argument(fullName="deletions_default_quality",shortName="ddq",doc="default quality for the base deletions covariate",required=false,exclusiveOf="",validation="")
/** minimum quality for the bases in the tail of the reads to be considered */
@Argument(fullName="low_quality_tail",shortName="lqt",doc="minimum quality for the bases in the tail of the reads to be considered",required=false,exclusiveOf="",validation="")
/** number of distinct quality scores in the quantized output */
@Argument(fullName="quantizing_levels",shortName="ql",doc="number of distinct quality scores in the quantized output",required=false,exclusiveOf="",validation="")
@Argument(fullName="sort_by_all_columns",shortName="sortAllCols",doc="Sort the rows in the tables of reports",required=false,exclusiveOf="",validation="")
/** If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid. */
@Argument(fullName="default_platform",shortName="dP",doc="If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.",required=false,exclusiveOf="",validation="")
/** If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid. */
@Argument(fullName="force_platform",shortName="fP",doc="If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.",required=false,exclusiveOf="",validation="")
/** If provided, the read group of EVERY read will be forced to be the provided String. */
@Argument(fullName="force_readgroup",shortName="fRG",doc="If provided, the read group of EVERY read will be forced to be the provided String.",required=false,exclusiveOf="",validation="")
/** If provided, log all updates to the recalibration tables to the given file. For debugging/testing purposes only */
@Output(fullName="recal_table_update_log",shortName="recal_table_update_log",doc="If provided, log all updates to the recalibration tables to the given file. For debugging/testing purposes only",required=false,exclusiveOf="",validation="")
...
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@@ -126,19 +111,19 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
/** Max size of the k-mer context to be used for repeat covariates */
@Argument(fullName="max_str_unit_length",shortName="maxstr",doc="Max size of the k-mer context to be used for repeat covariates",required=false,exclusiveOf="",validation="")
/** Max number of repetitions to be used for repeat covariates */
@Argument(fullName="max_repeat_length",shortName="maxrep",doc="Max number of repetitions to be used for repeat covariates",required=false,exclusiveOf="",validation="")
/** Reduce memory usage in multi-threaded code at the expense of threading efficiency */
@Argument(fullName="lowMemoryMode",shortName="lowMemoryMode",doc="Reduce memory usage in multi-threaded code at the expense of threading efficiency",required=false,exclusiveOf="",validation="")
/** BQSR BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets */
@Argument(fullName="bqsrBAQGapOpenPenalty",shortName="bqsrBAQGOP",doc="BQSR BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets",required=false,exclusiveOf="",validation="")
@Argument(fullName="bqsrBAQGapOpenPenaltyFormat",shortName="",doc="Format string for bqsrBAQGapOpenPenalty",required=false,exclusiveOf="",validation="")
...
...
@@ -146,15 +131,15 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
/** Filter out reads with CIGAR containing the N operator, instead of failing with an error */
@Argument(fullName="filter_reads_with_N_cigar",shortName="filterRNC",doc="Filter out reads with CIGAR containing the N operator, instead of failing with an error",required=false,exclusiveOf="",validation="")
/** Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error */
@Argument(fullName="filter_mismatching_base_and_quals",shortName="filterMBQ",doc="Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error",required=false,exclusiveOf="",validation="")
/** Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error */
@Argument(fullName="filter_bases_not_stored",shortName="filterNoBases",doc="Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error",required=false,exclusiveOf="",validation="")