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comparison variant_recalibrator.xml @ 0:340633249b3d draft

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author bgruening
date Mon, 02 Dec 2013 06:18:36 -0500
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1 <tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="0.0.7">
2 <description></description>
3 <expand macro="requirements" />
4 <macros>
5 <import>gatk2_macros.xml</import>
6 </macros>
7 <command interpreter="python">
8 gatk2_wrapper.py
9 --stdout "${output_log}"
10 #for $var_count, $variant in enumerate( $reference_source.variants ):
11 -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
12 #end for
13 -p '
14 @JAR_PATH@
15 -T "VariantRecalibrator"
16 \$GATK2_SITE_OPTIONS
17
18 @THREADS@
19
20 #if $reference_source.reference_source_selector != "history":
21 -R "${reference_source.ref_file.fields.path}"
22 #end if
23 --recal_file "${output_recal}"
24 --tranches_file "${output_tranches}"
25 --rscript_file "${output_rscript}"
26 '
27
28 #set $rod_binding_names = dict()
29 #for $rod_binding in $rod_bind:
30 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
31 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
32 #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
33 #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
34 #else
35 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
36 #end if
37 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
38 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
39 -d "--resource:${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[$rod_bind_name]}"
40 #else:
41 -d "--resource:${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]}"
42 #end if
43 #end for
44
45 #include source=$standard_gatk_options#
46
47 ##start analysis specific options
48 -p '
49 #if str( $annotations ) != "None":
50 #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ):
51 --use_annotation "${annotation}"
52 #end for
53 #end if
54 #for $additional_annotation in $additional_annotations:
55 --use_annotation "${additional_annotation.additional_annotation_name}"
56 #end for
57 --mode "${mode}"
58 '
59
60 #if $analysis_param_type.analysis_param_type_selector == "advanced":
61 -p '
62 --maxGaussians "${analysis_param_type.max_gaussians}"
63 --maxIterations "${analysis_param_type.max_iterations}"
64 --numKMeans "${analysis_param_type.num_k_means}"
65 --stdThreshold "${analysis_param_type.std_threshold}"
66 --qualThreshold "${analysis_param_type.qual_threshold}"
67 --shrinkage "${analysis_param_type.shrinkage}"
68 --dirichlet "${analysis_param_type.dirichlet}"
69 --priorCounts "${analysis_param_type.prior_counts}"
70 #if str( $analysis_param_type.bad_variant_selector.bad_variant_selector_type ) == 'percent':
71 --percentBadVariants "${analysis_param_type.bad_variant_selector.percent_bad_variants}"
72 #else:
73 --minNumBadVariants "${analysis_param_type.bad_variant_selector.min_num_bad_variants}"
74 #end if
75 --target_titv "${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 --ts_filter_level "${analysis_param_type.ts_filter_level}"
87 '
88 #end if
89
90
91 &amp;&amp;
92 mv "${output_rscript}.pdf" "${output_tranches_pdf}"
93
94 </command>
95 <inputs>
96 <conditional name="reference_source">
97 <expand macro="reference_source_selector_param" />
98 <when value="cached">
99 <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
100 <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
101 </repeat>
102 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
103 <options from_data_table="gatk_picard_indexes">
104 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
105 </options>
106 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
107 </param>
108 </when>
109 <when value="history"> <!-- FIX ME!!!! -->
110 <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
111 <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
112 </repeat>
113 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
114 </when>
115 </conditional>
116
117 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;">
118 <conditional name="rod_bind_type">
119 <param name="rod_bind_type_selector" type="select" label="Binding Type">
120 <option value="dbsnp" selected="True">dbSNP</option>
121 <option value="variant">Variants</option>
122 <option value="snps">SNPs</option>
123 <option value="indels">INDELs</option>
124 <option value="hapmap">HapMap</option>
125 <option value="omni">OMNI</option>
126 <option value="mask">Mask</option>
127 <option value="custom">Custom</option>
128 <option value="comp">Comp</option>
129 </param>
130 <when value="variant">
131 <param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
132 <conditional name="rod_training_type">
133 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
134 <option value="is_training_truth_known">Set training/truth/known sites</option>
135 <option value="not_training_truth_known" selected="True">Don't Set options</option>
136 </param>
137 <when value="not_training_truth_known">
138 <!-- do nothing here -->
139 </when>
140 <when value="is_training_truth_known">
141 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
142 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
143 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
144 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
145 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
146 </when>
147 </conditional>
148 </when>
149 <when value="comp">
150 <param name="input_rod" type="data" format="vcf" label="ROD file" />
151 <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
152 <conditional name="rod_training_type">
153 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
154 <option value="is_training_truth_known">Set training/truth/known sites</option>
155 <option value="not_training_truth_known" selected="True">Don't Set options</option>
156 </param>
157 <when value="not_training_truth_known">
158 <!-- do nothing here -->
159 </when>
160 <when value="is_training_truth_known">
161 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
162 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
163 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
164 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
165 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
166 </when>
167 </conditional>
168 </when>
169 <when value="mask">
170 <param name="input_rod" type="data" format="vcf" label="ROD file" />
171 <conditional name="rod_training_type">
172 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
173 <option value="is_training_truth_known">Set training/truth/known sites</option>
174 <option value="not_training_truth_known" selected="True">Don't Set options</option>
175 </param>
176 <when value="not_training_truth_known">
177 <!-- do nothing here -->
178 </when>
179 <when value="is_training_truth_known">
180 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
181 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
182 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
183 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
184 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
185 </when>
186 </conditional>
187 </when>
188 <when value="dbsnp">
189 <param name="input_rod" type="data" format="vcf" label="ROD file" />
190 <conditional name="rod_training_type">
191 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
192 <option value="is_training_truth_known">Set training/truth/known sites</option>
193 <option value="not_training_truth_known" selected="True">Don't Set options</option>
194 </param>
195 <when value="not_training_truth_known">
196 <!-- do nothing here -->
197 </when>
198 <when value="is_training_truth_known">
199 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
200 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
201 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
202 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
203 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
204 </when>
205 </conditional>
206 </when>
207 <when value="snps">
208 <param name="input_rod" type="data" format="vcf" label="ROD file" />
209 <conditional name="rod_training_type">
210 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
211 <option value="is_training_truth_known">Set training/truth/known sites</option>
212 <option value="not_training_truth_known" selected="True">Don't Set options</option>
213 </param>
214 <when value="not_training_truth_known">
215 <!-- do nothing here -->
216 </when>
217 <when value="is_training_truth_known">
218 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
219 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
220 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
221 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
222 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
223 </when>
224 </conditional>
225 </when>
226 <when value="hapmap">
227 <param name="input_rod" type="data" format="vcf" label="ROD file" />
228 <conditional name="rod_training_type">
229 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
230 <option value="is_training_truth_known">Set training/truth/known sites</option>
231 <option value="not_training_truth_known" selected="True">Don't Set options</option>
232 </param>
233 <when value="not_training_truth_known">
234 <!-- do nothing here -->
235 </when>
236 <when value="is_training_truth_known">
237 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
238 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
239 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
240 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
241 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
242 </when>
243 </conditional>
244 </when>
245 <when value="omni">
246 <param name="input_rod" type="data" format="vcf" label="ROD file" />
247 <conditional name="rod_training_type">
248 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
249 <option value="is_training_truth_known">Set training/truth/known sites</option>
250 <option value="not_training_truth_known" selected="True">Don't Set options</option>
251 </param>
252 <when value="not_training_truth_known">
253 <!-- do nothing here -->
254 </when>
255 <when value="is_training_truth_known">
256 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
257 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
258 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
259 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
260 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
261 </when>
262 </conditional>
263 </when>
264 <when value="indels">
265 <param name="input_rod" type="data" format="vcf" label="ROD file" />
266 <conditional name="rod_training_type">
267 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
268 <option value="is_training_truth_known">Set training/truth/known sites</option>
269 <option value="not_training_truth_known" selected="True">Don't Set options</option>
270 </param>
271 <when value="not_training_truth_known">
272 <!-- do nothing here -->
273 </when>
274 <when value="is_training_truth_known">
275 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
276 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
277 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
278 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
279 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
280 </when>
281 </conditional>
282 </when>
283 <when value="custom">
284 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
285 <param name="input_rod" type="data" format="vcf" label="ROD file" />
286 <conditional name="rod_training_type">
287 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
288 <option value="is_training_truth_known">Set training/truth/known sites</option>
289 <option value="not_training_truth_known" selected="True">Don't Set options</option>
290 </param>
291 <when value="not_training_truth_known">
292 <!-- do nothing here -->
293 </when>
294 <when value="is_training_truth_known">
295 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
296 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
297 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
298 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
299 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
300 </when>
301 </conditional>
302 </when>
303 </conditional>
304 </repeat>
305
306 <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;">
307 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
308 <options from_data_table="gatk2_annotations">
309 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
310 <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
311 </options>
312 </param>
313
314 <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
315 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
316 </repeat>
317
318 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
319 <option value="SNP" selected="True">SNP</option>
320 <option value="INDEL">INDEL</option>
321 <option value="BOTH">BOTH</option>
322 </param>
323
324 <expand macro="gatk_param_type_conditional" />
325
326 <expand macro="analysis_type_conditional">
327 <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;"/>
328 <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;"/>
329 <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;"/>
330 <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;"/>
331 <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;"/>
332 <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &amp;lt;shrinkage&amp;gt;"/>
333 <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &amp;lt;dirichlet&amp;gt;"/>
334 <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;"/>
335 <conditional name="bad_variant_selector">
336 <param name="bad_variant_selector_type" type="select" label="How to specify bad variants">
337 <option value="percent" selected="True">Percent</option>
338 <option value="min_num">Number</option>
339 </param>
340 <when value="percent">
341 <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;"/>
342 </when>
343 <when value="min_num">
344 <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;"/>
345 </when>
346 </conditional>
347 <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;"/>
348 <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;"/>
349 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &amp;lt;ignore_filter&amp;gt;">
350 <conditional name="ignore_filter_type">
351 <param name="ignore_filter_type_selector" type="select" label="Filter Type">
352 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
353 <option value="LowQual" >LowQual</option>
354 <option value="custom" selected="True">Other</option>
355 </param>
356 <when value="custom">
357 <param name="filter_name" type="text" value="" label="Filter name"/>
358 </when>
359 <when value="HARD_TO_VALIDATE" />
360 <when value="LowQual" />
361 </conditional>
362 </repeat>
363 <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;"/>
364 </expand>
365 </inputs>
366 <outputs>
367 <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" />
368 <data format="gatk_tranche" name="output_tranches" label="${tool.name} on ${on_string} (Tranches File)" />
369 <data format="txt" name="output_rscript" label="${tool.name} on ${on_string} (RScript File)" />
370 <data format="pdf" name="output_tranches_pdf" label="${tool.name} on ${on_string} (PDF File)" />
371 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
372 </outputs>
373 <tests>
374 <!-- ADD TESTS -->
375 </tests>
376 <help>
377 **What it does**
378
379 Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score
380
381 For more information on using the VariantRecalibrator module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_VariantRecalibrator.html&gt;`_.
382
383 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
384
385 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
386
387 ------
388
389 **Inputs**
390
391 GenomeAnalysisTK: VariantRecalibrator accepts a variant input file.
392
393
394 **Outputs**
395
396 The output is in VCF format.
397
398
399 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
400
401 -------
402
403 **Settings**::
404
405
406 tranches_file The output tranches file used by ApplyRecalibration
407 use_annotation The names of the annotations which should used for calculations
408 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)
409 maxGaussians The maximum number of Gaussians to try during variational Bayes algorithm
410 maxIterations The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.
411 numKMeans The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.
412 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.
413 qualThreshold If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model.
414 shrinkage The shrinkage parameter in variational Bayes algorithm.
415 dirichlet The dirichlet parameter in variational Bayes algorithm.
416 priorCounts The number of prior counts to use in variational Bayes algorithm.
417 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.
418 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.
419 recal_file The output recal file used by ApplyRecalibration
420 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!
421 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)
422 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file
423 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
424 rscript_file The output rscript file generated by the VQSR to aid in visualization of the input data and learned model
425 path_to_resources Path to resources folder holding the Sting R scripts.
426 ts_filter_level The truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots
427
428 @CITATION_SECTION@
429 </help>
430 </tool>