15
+ − 1 <tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.1">
+ − 2 <description></description>
+ − 3 <macros>
+ − 4 <import>gatk2_macros.xml</import>
+ − 5 </macros>
+ − 6 <expand macro="requirements">
+ − 7 <requirement type="package" version="0.9.3">ggplot2</requirement>
+ − 8 </expand>
+ − 9 <expand macro="version_command" />
+ − 10 <command interpreter="python">
+ − 11 gatk2_wrapper.py
+ − 12 --stdout "${output_log}"
+ − 13 #for $var_count, $variant in enumerate( $reference_source.input_variants ):
+ − 14 -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
+ − 15 #end for
+ − 16 -p '
+ − 17 @JAR_PATH@
+ − 18 -T "VariantRecalibrator"
+ − 19 \$GATK2_SITE_OPTIONS
+ − 20
+ − 21 @THREADS@
+ − 22
+ − 23 #if $reference_source.reference_source_selector != "history":
+ − 24 -R "${reference_source.ref_file.fields.path}"
+ − 25 #end if
+ − 26 --recal_file "${output_recal}"
+ − 27 --tranches_file "${output_tranches}"
+ − 28 --rscript_file "${output_rscript}"
+ − 29 '
+ − 30
+ − 31 #set $rod_binding_names = dict()
+ − 32 #for $rod_binding in $rod_bind:
+ − 33 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
+ − 34 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
+ − 35 #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
+ − 36 #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
+ − 37 #else
+ − 38 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
+ − 39 #end if
+ − 40 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
+ − 41 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
+ − 42 -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+ − 43 #else:
+ − 44 -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+ − 45 #end if
+ − 46 #end for
+ − 47
+ − 48 #include source=$standard_gatk_options#
+ − 49
+ − 50 ##start analysis specific options
+ − 51 -p '
+ − 52 #if str( $annotations ) != "None":
+ − 53 #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ):
+ − 54 --use_annotation "${annotation}"
+ − 55 #end for
+ − 56 #end if
+ − 57 #for $additional_annotation in $additional_annotations:
+ − 58 --use_annotation "${additional_annotation.additional_annotation_name}"
+ − 59 #end for
+ − 60 --mode "${mode}"
+ − 61 '
+ − 62
+ − 63 #if $analysis_param_type.analysis_param_type_selector == "advanced":
+ − 64 -p '
+ − 65 --maxGaussians "${analysis_param_type.max_gaussians}"
+ − 66 --maxIterations "${analysis_param_type.max_iterations}"
+ − 67 --numKMeans "${analysis_param_type.num_k_means}"
+ − 68 --stdThreshold "${analysis_param_type.std_threshold}"
+ − 69 --shrinkage "${analysis_param_type.shrinkage}"
+ − 70 --dirichlet "${analysis_param_type.dirichlet}"
+ − 71 --priorCounts "${analysis_param_type.prior_counts}"
+ − 72
+ − 73 --minNumBadVariants "${analysis_param_type.min_num_bad_variants}"
+ − 74
+ − 75 --target_titv "${analysis_param_type.target_titv}"
+ − 76 #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ]
+ − 77 --TStranche "${tranche}"
+ − 78 #end for
+ − 79 #for $ignore_filter in $analysis_param_type.ignore_filters:
+ − 80 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
+ − 81 #if $ignore_filter_name == "custom":
+ − 82 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
+ − 83 #end if
+ − 84 --ignore_filter "${ignore_filter_name}"
+ − 85 #end for
+ − 86 '
+ − 87 #end if
+ − 88
+ − 89 &&
+ − 90 mv "${output_rscript}.pdf" "${output_tranches_pdf}"
+ − 91
+ − 92 </command>
+ − 93 <inputs>
+ − 94 <conditional name="reference_source">
+ − 95 <expand macro="reference_source_selector_param" />
+ − 96 <when value="cached">
+ − 97 <expand macro="input_variants" />
+ − 98 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
+ − 99 <options from_data_table="gatk2_picard_indexes">
+ − 100 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
+ − 101 </options>
+ − 102 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+ − 103 </param>
+ − 104 </when>
+ − 105 <when value="history"> <!-- FIX ME!!!! -->
+ − 106 <expand macro="input_variants" />
+ − 107 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
+ − 108 </when>
+ − 109 </conditional>
+ − 110
+ − 111 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &lt;resource&gt;" min="2">
+ − 112 <conditional name="rod_bind_type">
+ − 113 <param name="rod_bind_type_selector" type="select" label="Binding Type">
+ − 114 <option value="dbsnp" selected="True">dbSNP</option>
+ − 115 <option value="variant">Variants</option>
+ − 116 <option value="snps">SNPs</option>
+ − 117 <option value="indels">INDELs</option>
+ − 118 <option value="hapmap">HapMap</option>
+ − 119 <option value="omni">OMNI</option>
+ − 120 <option value="mask">Mask</option>
+ − 121 <option value="custom">Custom</option>
+ − 122 <option value="comp">Comp</option>
+ − 123 </param>
+ − 124 <when value="variant">
+ − 125 <param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
+ − 126 <conditional name="rod_training_type">
+ − 127 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+ − 128 <option value="is_training_truth_known">Set training/truth/known sites</option>
+ − 129 <option value="not_training_truth_known" selected="True">Don't Set options</option>
+ − 130 </param>
+ − 131 <when value="not_training_truth_known">
+ − 132 <!-- do nothing here -->
+ − 133 </when>
+ − 134 <when value="is_training_truth_known">
+ − 135 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+ − 136 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+ − 137 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+ − 138 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+ − 139 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+ − 140 </when>
+ − 141 </conditional>
+ − 142 </when>
+ − 143 <when value="comp">
+ − 144 <param name="input_rod" type="data" format="vcf" label="ROD file" />
+ − 145 <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
+ − 146 <conditional name="rod_training_type">
+ − 147 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+ − 148 <option value="is_training_truth_known">Set training/truth/known sites</option>
+ − 149 <option value="not_training_truth_known" selected="True">Don't Set options</option>
+ − 150 </param>
+ − 151 <when value="not_training_truth_known">
+ − 152 <!-- do nothing here -->
+ − 153 </when>
+ − 154 <when value="is_training_truth_known">
+ − 155 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+ − 156 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+ − 157 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+ − 158 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+ − 159 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+ − 160 </when>
+ − 161 </conditional>
+ − 162 </when>
+ − 163 <when value="mask">
+ − 164 <param name="input_rod" type="data" format="vcf" label="ROD file" />
+ − 165 <conditional name="rod_training_type">
+ − 166 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+ − 167 <option value="is_training_truth_known">Set training/truth/known sites</option>
+ − 168 <option value="not_training_truth_known" selected="True">Don't Set options</option>
+ − 169 </param>
+ − 170 <when value="not_training_truth_known">
+ − 171 <!-- do nothing here -->
+ − 172 </when>
+ − 173 <when value="is_training_truth_known">
+ − 174 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+ − 175 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+ − 176 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+ − 177 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+ − 178 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+ − 179 </when>
+ − 180 </conditional>
+ − 181 </when>
+ − 182 <when value="dbsnp">
+ − 183 <param name="input_rod" type="data" format="vcf" label="ROD file" />
+ − 184 <conditional name="rod_training_type">
+ − 185 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+ − 186 <option value="is_training_truth_known">Set training/truth/known sites</option>
+ − 187 <option value="not_training_truth_known" selected="True">Don't Set options</option>
+ − 188 </param>
+ − 189 <when value="not_training_truth_known">
+ − 190 <!-- do nothing here -->
+ − 191 </when>
+ − 192 <when value="is_training_truth_known">
+ − 193 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+ − 194 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+ − 195 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+ − 196 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+ − 197 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+ − 198 </when>
+ − 199 </conditional>
+ − 200 </when>
+ − 201 <when value="snps">
+ − 202 <param name="input_rod" type="data" format="vcf" label="ROD file" />
+ − 203 <conditional name="rod_training_type">
+ − 204 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+ − 205 <option value="is_training_truth_known">Set training/truth/known sites</option>
+ − 206 <option value="not_training_truth_known" selected="True">Don't Set options</option>
+ − 207 </param>
+ − 208 <when value="not_training_truth_known">
+ − 209 <!-- do nothing here -->
+ − 210 </when>
+ − 211 <when value="is_training_truth_known">
+ − 212 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+ − 213 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+ − 214 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+ − 215 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+ − 216 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+ − 217 </when>
+ − 218 </conditional>
+ − 219 </when>
+ − 220 <when value="hapmap">
+ − 221 <param name="input_rod" type="data" format="vcf" label="ROD file" />
+ − 222 <conditional name="rod_training_type">
+ − 223 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+ − 224 <option value="is_training_truth_known">Set training/truth/known sites</option>
+ − 225 <option value="not_training_truth_known" selected="True">Don't Set options</option>
+ − 226 </param>
+ − 227 <when value="not_training_truth_known">
+ − 228 <!-- do nothing here -->
+ − 229 </when>
+ − 230 <when value="is_training_truth_known">
+ − 231 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+ − 232 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+ − 233 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+ − 234 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+ − 235 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+ − 236 </when>
+ − 237 </conditional>
+ − 238 </when>
+ − 239 <when value="omni">
+ − 240 <param name="input_rod" type="data" format="vcf" label="ROD file" />
+ − 241 <conditional name="rod_training_type">
+ − 242 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+ − 243 <option value="is_training_truth_known">Set training/truth/known sites</option>
+ − 244 <option value="not_training_truth_known" selected="True">Don't Set options</option>
+ − 245 </param>
+ − 246 <when value="not_training_truth_known">
+ − 247 <!-- do nothing here -->
+ − 248 </when>
+ − 249 <when value="is_training_truth_known">
+ − 250 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+ − 251 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+ − 252 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+ − 253 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+ − 254 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+ − 255 </when>
+ − 256 </conditional>
+ − 257 </when>
+ − 258 <when value="indels">
+ − 259 <param name="input_rod" type="data" format="vcf" label="ROD file" />
+ − 260 <conditional name="rod_training_type">
+ − 261 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+ − 262 <option value="is_training_truth_known">Set training/truth/known sites</option>
+ − 263 <option value="not_training_truth_known" selected="True">Don't Set options</option>
+ − 264 </param>
+ − 265 <when value="not_training_truth_known">
+ − 266 <!-- do nothing here -->
+ − 267 </when>
+ − 268 <when value="is_training_truth_known">
+ − 269 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+ − 270 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+ − 271 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+ − 272 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+ − 273 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+ − 274 </when>
+ − 275 </conditional>
+ − 276 </when>
+ − 277 <when value="custom">
+ − 278 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
+ − 279 <param name="input_rod" type="data" format="vcf" label="ROD file" />
+ − 280 <conditional name="rod_training_type">
+ − 281 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+ − 282 <option value="is_training_truth_known">Set training/truth/known sites</option>
+ − 283 <option value="not_training_truth_known" selected="True">Don't Set options</option>
+ − 284 </param>
+ − 285 <when value="not_training_truth_known">
+ − 286 <!-- do nothing here -->
+ − 287 </when>
+ − 288 <when value="is_training_truth_known">
+ − 289 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+ − 290 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+ − 291 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+ − 292 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+ − 293 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+ − 294 </when>
+ − 295 </conditional>
+ − 296 </when>
+ − 297 </conditional>
+ − 298 </repeat>
+ − 299
+ − 300 <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &lt;use_annotation&gt;">
+ − 301 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
+ − 302 <options from_data_table="gatk2_annotations">
+ − 303 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
+ − 304 <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
+ − 305 </options>
+ − 306 </param>
+ − 307
+ − 308 <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &lt;use_annotation&gt;">
+ − 309 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+ − 310 </repeat>
+ − 311
+ − 312 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;">
+ − 313 <option value="SNP" selected="True">SNP</option>
+ − 314 <option value="INDEL">INDEL</option>
+ − 315 <option value="BOTH">BOTH</option>
+ − 316 </param>
+ − 317
+ − 318 <expand macro="gatk_param_type_conditional" />
+ − 319
+ − 320 <expand macro="analysis_type_conditional">
+ − 321 <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="8" help="-mG,--maxGaussians &lt;maxGaussians&gt;"/>
+ − 322 <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="150" help="-mI,--maxIterations &lt;maxIterations&gt;"/>
+ − 323 <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="100" help="-nKM,--numKMeans &lt;numKMeans&gt;"/>
+ − 324 <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="10.0" help="-std,--stdThreshold &lt;stdThreshold&gt;"/>
+ − 325 <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &lt;shrinkage&gt;"/>
+ − 326 <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &lt;dirichlet&gt;"/>
+ − 327 <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0" help="-priorCounts,--priorCounts &lt;priorCounts&gt;"/>
+ − 328 <!--<param name="trustAllPolymorphic" type="boolean" label="trustAllPolymorphic" truevalue="-/-trustAllPolymorphic=true" falsevalue="-/-trustAllPolymorphic=false"
+ − 329 help="Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation. -trustAllPolymorphic" />-->
+ − 330 <param name="min_num_bad_variants" type="integer" label="Minimum number of worst scoring variants to use when building the Gaussian mixture model of bad variants" value="1000" help="--minNumBadVariants &lt;minNumBadVariants&gt;"/>
+ − 331 <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15" help="-titv,--target_titv &lt;target_titv&gt;"/>
+ − 332 <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0" help="-tranche,--TStranche &lt;TStranche&gt;"/>
+ − 333 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;">
+ − 334 <conditional name="ignore_filter_type">
+ − 335 <param name="ignore_filter_type_selector" type="select" label="Filter Type">
+ − 336 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
+ − 337 <option value="LowQual" >LowQual</option>
+ − 338 <option value="custom" selected="True">Other</option>
+ − 339 </param>
+ − 340 <when value="custom">
+ − 341 <param name="filter_name" type="text" value="" label="Filter name"/>
+ − 342 </when>
+ − 343 <when value="HARD_TO_VALIDATE" />
+ − 344 <when value="LowQual" />
+ − 345 </conditional>
+ − 346 </repeat>
+ − 347 </expand>
+ − 348 </inputs>
+ − 349 <outputs>
+ − 350 <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" />
+ − 351 <data format="gatk_tranche" name="output_tranches" label="${tool.name} on ${on_string} (Tranches File)" />
+ − 352 <data format="txt" name="output_rscript" label="${tool.name} on ${on_string} (RScript File)" />
+ − 353 <data format="pdf" name="output_tranches_pdf" label="${tool.name} on ${on_string} (PDF File)" />
+ − 354 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+ − 355 </outputs>
+ − 356 <tests>
+ − 357 <!-- ADD TESTS -->
+ − 358 </tests>
+ − 359 <help>
+ − 360 **What it does**
+ − 361
+ − 362 Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score
+ − 363
+ − 364 For more information on using the VariantRecalibrator module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_VariantRecalibrator.html>`_.
+ − 365
+ − 366 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_.
+ − 367
+ − 368 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
+ − 369
+ − 370 ------
+ − 371
+ − 372 **Inputs**
+ − 373
+ − 374 GenomeAnalysisTK: VariantRecalibrator accepts a variant input file.
+ − 375
+ − 376
+ − 377 **Outputs**
+ − 378
+ − 379 The output is in VCF format.
+ − 380
+ − 381
+ − 382 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
+ − 383
+ − 384 -------
+ − 385
+ − 386 **Settings**::
+ − 387
+ − 388
+ − 389 tranches_file The output tranches file used by ApplyRecalibration
+ − 390 use_annotation The names of the annotations which should used for calculations
+ − 391 mode Recalibration mode to employ: 1.) SNP for recalibrating only snps (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both snps and indels simultaneously. (SNP|INDEL|BOTH)
+ − 392 maxGaussians The maximum number of Gaussians to try during variational Bayes algorithm
+ − 393 maxIterations The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.
+ − 394 numKMeans The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.
+ − 395 stdThreshold If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model.
+ − 396 shrinkage The shrinkage parameter in variational Bayes algorithm.
+ − 397 dirichlet The dirichlet parameter in variational Bayes algorithm.
+ − 398 priorCounts The number of prior counts to use in variational Bayes algorithm.
+ − 399 minNumBadVariants The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants.
+ − 400 recal_file The output recal file used by ApplyRecalibration
+ − 401 target_titv The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!
+ − 402 TStranche The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)
+ − 403 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file
+ − 404 path_to_Rscript The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript
+ − 405 rscript_file The output rscript file generated by the VQSR to aid in visualization of the input data and learned model
+ − 406 path_to_resources Path to resources folder holding the Sting R scripts.
+ − 407
+ − 408 @CITATION_SECTION@
+ − 409 </help>
+ − 410 <expand macro="citations" />
+ − 411 </tool>