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/tools/gatk/variant_recalibrator.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.4">
  2  <description></description>
  3  <requirements>
  4      <requirement type="package" version="1.4">gatk</requirement>
  5  </requirements>
  6  <macros>
  7    <import>gatk_macros.xml</import>
  8  </macros>
  9  <command interpreter="python">gatk_wrapper.py
 10   --max_jvm_heap_fraction "1"
 11   --stdout "${output_log}"
 12   #for $var_count, $variant in enumerate( $reference_source.variants ):
 13      -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
 14   #end for
 15   -p 'java 
 16    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
 17    -T "VariantRecalibrator"
 18    --num_threads 4 ##hard coded, for now
 19    -et "NO_ET" ##ET no phone home
 20    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
 21    #if $reference_source.reference_source_selector != "history":
 22        -R "${reference_source.ref_file.fields.path}"
 23    #end if
 24    --recal_file "${output_recal}"
 25    --tranches_file "${output_tranches}"
 26    --rscript_file "${output_rscript}"
 27   '
 28    
 29    #set $rod_binding_names = dict()
 30    #for $rod_binding in $rod_bind:
 31        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
 32            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
 33        #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
 34            #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
 35        #else 
 36            #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
 37        #end if
 38        #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
 39        #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
 40            -d "--resource:${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[$rod_bind_name]}"
 41        #else:
 42            -d "--resource:${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]}"
 43        #end if
 44    #end for
 45    
 46    #include source=$standard_gatk_options#
 47    
 48    ##start analysis specific options
 49    -p '
 50    #if str( $annotations ) != "None":
 51        #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ):
 52            --use_annotation "${annotation}"
 53        #end for
 54    #end if
 55    #for $additional_annotation in $additional_annotations:
 56        --use_annotation "${additional_annotation.additional_annotation_name}"
 57    #end for
 58    --mode "${mode}"
 59    '
 60    
 61    #if $analysis_param_type.analysis_param_type_selector == "advanced":
 62        -p '
 63        --maxGaussians "${analysis_param_type.max_gaussians}"
 64        --maxIterations "${analysis_param_type.max_iterations}"
 65        --numKMeans "${analysis_param_type.num_k_means}"
 66        --stdThreshold "${analysis_param_type.std_threshold}"
 67        --qualThreshold "${analysis_param_type.qual_threshold}"
 68        --shrinkage "${analysis_param_type.shrinkage}"
 69        --dirichlet "${analysis_param_type.dirichlet}"
 70        --priorCounts "${analysis_param_type.prior_counts}"
 71        #if str( $analysis_param_type.bad_variant_selector.bad_variant_selector_type ) == 'percent':
 72            --percentBadVariants "${analysis_param_type.bad_variant_selector.percent_bad_variants}"
 73        #else:
 74            --minNumBadVariants "${analysis_param_type.bad_variant_selector.min_num_bad_variants}"
 75        #end if
 76        --target_titv "${analysis_param_type.target_titv}"
 77        #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ]
 78            --TStranche "${tranche}"
 79        #end for
 80        #for $ignore_filter in $analysis_param_type.ignore_filters:
 81            #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
 82            #if $ignore_filter_name == "custom":
 83              #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
 84            #end if
 85            --ignore_filter "${ignore_filter_name}"
 86        #end for
 87        --ts_filter_level "${analysis_param_type.ts_filter_level}"
 88        '
 89    #end if
 90    
 91    
 92    &amp;&amp;
 93    mv "${output_rscript}.pdf" "${output_tranches_pdf}"
 94    
 95  </command>
 96  <inputs>
 97    <conditional name="reference_source">
 98      <expand macro="reference_source_selector_param" />
 99      <when value="cached">
100        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
101          <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
102        </repeat>
103        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
104          <options from_data_table="gatk_picard_indexes">
105          <!--  <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
106          </options>
107          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
108        </param>
109      </when>
110      <when value="history"> <!-- FIX ME!!!! -->
111        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
112          <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
113        </repeat>
114        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
115      </when>
116    </conditional>
117    
118    <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;">
119        <conditional name="rod_bind_type">
120          <param name="rod_bind_type_selector" type="select" label="Binding Type">
121            <option value="dbsnp" selected="True">dbSNP</option>
122            <option value="variant">Variants</option>
123            <option value="snps">SNPs</option>
124            <option value="indels">INDELs</option>
125            <option value="hapmap">HapMap</option>
126            <option value="omni">OMNI</option>
127            <option value="mask">Mask</option>
128            <option value="custom">Custom</option>
129            <option value="comp">Comp</option>
130          </param>
131          <when value="variant">
132              <param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
133              <conditional name="rod_training_type">
134                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
135                      <option value="is_training_truth_known">Set training/truth/known sites</option>
136                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
137                  </param>
138                  <when value="not_training_truth_known">
139                      <!-- do nothing here -->
140                  </when>
141                  <when value="is_training_truth_known">
142                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
143                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
144                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
145                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
146                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
147                  </when>
148              </conditional>
149          </when>
150          <when value="comp">
151              <param name="input_rod" type="data" format="vcf" label="ROD file" />
152              <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
153              <conditional name="rod_training_type">
154                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
155                      <option value="is_training_truth_known">Set training/truth/known sites</option>
156                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
157                  </param>
158                  <when value="not_training_truth_known">
159                      <!-- do nothing here -->
160                  </when>
161                  <when value="is_training_truth_known">
162                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
163                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
164                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
165                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
166                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
167                  </when>
168              </conditional>
169          </when>
170          <when value="mask">
171              <param name="input_rod" type="data" format="vcf" label="ROD file" />
172              <conditional name="rod_training_type">
173                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
174                      <option value="is_training_truth_known">Set training/truth/known sites</option>
175                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
176                  </param>
177                  <when value="not_training_truth_known">
178                      <!-- do nothing here -->
179                  </when>
180                  <when value="is_training_truth_known">
181                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
182                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
183                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
184                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
185                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
186                  </when>
187              </conditional>
188          </when>          
189          <when value="dbsnp">
190              <param name="input_rod" type="data" format="vcf" label="ROD file" />
191              <conditional name="rod_training_type">
192                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
193                      <option value="is_training_truth_known">Set training/truth/known sites</option>
194                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
195                  </param>
196                  <when value="not_training_truth_known">
197                      <!-- do nothing here -->
198                  </when>
199                  <when value="is_training_truth_known">
200                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
201                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
202                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
203                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
204                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
205                  </when>
206              </conditional>
207          </when>
208          <when value="snps">
209              <param name="input_rod" type="data" format="vcf" label="ROD file" />
210              <conditional name="rod_training_type">
211                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
212                      <option value="is_training_truth_known">Set training/truth/known sites</option>
213                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
214                  </param>
215                  <when value="not_training_truth_known">
216                      <!-- do nothing here -->
217                  </when>
218                  <when value="is_training_truth_known">
219                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
220                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
221                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
222                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
223                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
224                  </when>
225              </conditional>
226          </when>
227          <when value="hapmap">
228              <param name="input_rod" type="data" format="vcf" label="ROD file" />
229              <conditional name="rod_training_type">
230                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
231                      <option value="is_training_truth_known">Set training/truth/known sites</option>
232                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
233                  </param>
234                  <when value="not_training_truth_known">
235                      <!-- do nothing here -->
236                  </when>
237                  <when value="is_training_truth_known">
238                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
239                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
240                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
241                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
242                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
243                  </when>
244              </conditional>
245          </when>
246          <when value="omni">
247              <param name="input_rod" type="data" format="vcf" label="ROD file" />
248              <conditional name="rod_training_type">
249                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
250                      <option value="is_training_truth_known">Set training/truth/known sites</option>
251                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
252                  </param>
253                  <when value="not_training_truth_known">
254                      <!-- do nothing here -->
255                  </when>
256                  <when value="is_training_truth_known">
257                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
258                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
259                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
260                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
261                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
262                  </when>
263              </conditional>
264          </when>
265          <when value="indels">
266              <param name="input_rod" type="data" format="vcf" label="ROD file" />
267              <conditional name="rod_training_type">
268                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
269                      <option value="is_training_truth_known">Set training/truth/known sites</option>
270                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
271                  </param>
272                  <when value="not_training_truth_known">
273                      <!-- do nothing here -->
274                  </when>
275                  <when value="is_training_truth_known">
276                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
277                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
278                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
279                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
280                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
281                  </when>
282              </conditional>
283          </when>
284          <when value="custom">
285              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
286              <param name="input_rod" type="data" format="vcf" label="ROD file" />
287              <conditional name="rod_training_type">
288                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
289                      <option value="is_training_truth_known">Set training/truth/known sites</option>
290                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
291                  </param>
292                  <when value="not_training_truth_known">
293                      <!-- do nothing here -->
294                  </when>
295                  <when value="is_training_truth_known">
296                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
297                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
298                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
299                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
300                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
301                  </when>
302              </conditional>
303          </when>
304        </conditional>
305    </repeat>
306    
307    <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
308      <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
309      <options from_data_table="gatk_annotations">
310        <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
311        <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
312      </options>
313    </param>
314    
315    <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
316      <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
317    </repeat>
318    
319    <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
320        <option value="SNP" selected="True">SNP</option>
321        <option value="INDEL">INDEL</option>
322        <option value="BOTH">BOTH</option>
323    </param>
324    
325    <expand macro="gatk_param_type_conditional" />
326    
327    <expand macro="analysis_type_conditional">
328        <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10" help="-mG,--maxGaussians &amp;lt;maxGaussians&amp;gt;"/>
329        <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100" help="-mI,--maxIterations &amp;lt;maxIterations&amp;gt;"/>
330        <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="30" help="-nKM,--numKMeans &amp;lt;numKMeans&amp;gt;"/>
331        <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="8.0" help="-std,--stdThreshold &amp;lt;stdThreshold&amp;gt;"/>
332        <param name="qual_threshold" type="float" label="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model." value="80.0" help="-qual,--qualThreshold &amp;lt;qualThreshold&amp;gt;"/>
333        <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &amp;lt;shrinkage&amp;gt;"/>
334        <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &amp;lt;dirichlet&amp;gt;"/>
335        <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0" help="-priorCounts,--priorCounts &amp;lt;priorCounts&amp;gt;"/>
336        <conditional name="bad_variant_selector">
337          <param name="bad_variant_selector_type" type="select" label="How to specify bad variants">
338            <option value="percent" selected="True">Percent</option>
339            <option value="min_num">Number</option>
340          </param>
341          <when value="percent">
342            <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03" help="-percentBad,--percentBadVariants &amp;lt;percentBadVariants&amp;gt;"/>
343          </when>
344          <when value="min_num">
345            <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000" help="-minNumBad,--minNumBadVariants &amp;lt;minNumBadVariants&amp;gt;"/>
346          </when>
347        </conditional>
348        <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 &amp;lt;target_titv&amp;gt;"/>
349        <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 &amp;lt;TStranche&amp;gt;"/>
350        <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &amp;lt;ignore_filter&amp;gt;">
351          <conditional name="ignore_filter_type">
352            <param name="ignore_filter_type_selector" type="select" label="Filter Type">
353              <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
354              <option value="LowQual" >LowQual</option>
355              <option value="custom" selected="True">Other</option>
356            </param>
357            <when value="custom">
358              <param name="filter_name" type="text" value="" label="Filter name"/>
359            </when>
360            <when value="HARD_TO_VALIDATE" />
361            <when value="LowQual" />
362          </conditional>
363        </repeat>
364        <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &amp;lt;ts_filter_level&amp;gt;"/>
365    </expand>
366  </inputs>
367  <outputs>
368    <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" />
369    <data format="gatk_tranche" name="output_tranches" label="${tool.name} on ${on_string} (Tranches File)" />
370    <data format="txt" name="output_rscript" label="${tool.name} on ${on_string} (RScript File)" />
371    <data format="pdf" name="output_tranches_pdf" label="${tool.name} on ${on_string} (PDF File)" />
372    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
373  </outputs>
374  <tests>
375      <!-- ADD TESTS -->
376  </tests>
377  <help>
378**What it does**
379
380Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score
381
382For more information on using the VariantRecalibrator module, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration&gt;`_.
383
384To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
385
386If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
387
388------
389
390**Inputs**
391
392GenomeAnalysisTK: VariantRecalibrator accepts a variant input file.
393
394
395**Outputs**
396
397The output is in VCF format.
398
399
400Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
401
402-------
403
404**Settings**::
405
406
407 tranches_file         The output tranches file used by ApplyRecalibration
408 use_annotation        The names of the annotations which should used for calculations
409 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)
410 maxGaussians          The maximum number of Gaussians to try during variational Bayes algorithm
411 maxIterations         The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.
412 numKMeans             The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.
413 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.
414 qualThreshold         If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model.
415 shrinkage             The shrinkage parameter in variational Bayes algorithm.
416 dirichlet             The dirichlet parameter in variational Bayes algorithm.
417 priorCounts           The number of prior counts to use in variational Bayes algorithm.
418 percentBadVariants    What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent.
419 minNumBadVariants     The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary.
420 recal_file            The output recal file used by ApplyRecalibration
421 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!
422 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)
423 ignore_filter         If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file
424 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
425 rscript_file          The output rscript file generated by the VQSR to aid in visualization of the input data and learned model
426 path_to_resources     Path to resources folder holding the Sting R scripts.
427 ts_filter_level       The truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots
428
429@CITATION_SECTION@
430  </help>
431</tool>