--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_recalibrator.xml	Mon Dec 02 06:18:36 2013 -0500
@@ -0,0 +1,430 @@
+<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="0.0.7">
+  <description></description>
+  <expand macro="requirements" />
+  <macros>
+    <import>gatk2_macros.xml</import>
+  </macros>
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    #for $var_count, $variant in enumerate( $reference_source.variants ):
+        -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
+    #end for
+    -p '
+    @JAR_PATH@
+    -T "VariantRecalibrator"
+    \$GATK2_SITE_OPTIONS
+
+    @THREADS@
+
+    #if $reference_source.reference_source_selector != "history":
+        -R "${reference_source.ref_file.fields.path}"
+    #end if
+    --recal_file "${output_recal}"
+    --tranches_file "${output_tranches}"
+    --rscript_file "${output_rscript}"
+   '
+    
+    #set $rod_binding_names = dict()
+    #for $rod_binding in $rod_bind:
+        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
+            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
+        #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
+            #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
+        #else 
+            #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
+        #end if
+        #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
+        #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
+            -d "--resource:${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[$rod_bind_name]}"
+        #else:
+            -d "--resource:${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]}"
+        #end if
+    #end for
+    
+    #include source=$standard_gatk_options#
+    
+    ##start analysis specific options
+    -p '
+    #if str( $annotations ) != "None":
+        #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ):
+            --use_annotation "${annotation}"
+        #end for
+    #end if
+    #for $additional_annotation in $additional_annotations:
+        --use_annotation "${additional_annotation.additional_annotation_name}"
+    #end for
+    --mode "${mode}"
+    '
+    
+    #if $analysis_param_type.analysis_param_type_selector == "advanced":
+        -p '
+        --maxGaussians "${analysis_param_type.max_gaussians}"
+        --maxIterations "${analysis_param_type.max_iterations}"
+        --numKMeans "${analysis_param_type.num_k_means}"
+        --stdThreshold "${analysis_param_type.std_threshold}"
+        --qualThreshold "${analysis_param_type.qual_threshold}"
+        --shrinkage "${analysis_param_type.shrinkage}"
+        --dirichlet "${analysis_param_type.dirichlet}"
+        --priorCounts "${analysis_param_type.prior_counts}"
+        #if str( $analysis_param_type.bad_variant_selector.bad_variant_selector_type ) == 'percent':
+            --percentBadVariants "${analysis_param_type.bad_variant_selector.percent_bad_variants}"
+        #else:
+            --minNumBadVariants "${analysis_param_type.bad_variant_selector.min_num_bad_variants}"
+        #end if
+        --target_titv "${analysis_param_type.target_titv}"
+        #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ]
+            --TStranche "${tranche}"
+        #end for
+        #for $ignore_filter in $analysis_param_type.ignore_filters:
+            #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
+            #if $ignore_filter_name == "custom":
+              #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
+            #end if
+            --ignore_filter "${ignore_filter_name}"
+        #end for
+        --ts_filter_level "${analysis_param_type.ts_filter_level}"
+        '
+    #end if
+    
+    
+    &amp;&amp;
+    mv "${output_rscript}.pdf" "${output_tranches_pdf}"
+    
+  </command>
+  <inputs>
+    <conditional name="reference_source">
+      <expand macro="reference_source_selector_param" />
+      <when value="cached">
+        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
+          <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
+        </repeat>
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
+          <options from_data_table="gatk_picard_indexes">
+          <!--  <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
+          </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+        </param>
+      </when>
+      <when value="history"> <!-- FIX ME!!!! -->
+        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
+          <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
+        </repeat>
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
+      </when>
+    </conditional>
+    
+    <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;">
+        <conditional name="rod_bind_type">
+          <param name="rod_bind_type_selector" type="select" label="Binding Type">
+            <option value="dbsnp" selected="True">dbSNP</option>
+            <option value="variant">Variants</option>
+            <option value="snps">SNPs</option>
+            <option value="indels">INDELs</option>
+            <option value="hapmap">HapMap</option>
+            <option value="omni">OMNI</option>
+            <option value="mask">Mask</option>
+            <option value="custom">Custom</option>
+            <option value="comp">Comp</option>
+          </param>
+          <when value="variant">
+              <param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>
+          <when value="comp">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+              <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>
+          <when value="mask">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>          
+          <when value="dbsnp">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>
+          <when value="snps">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>
+          <when value="hapmap">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>
+          <when value="omni">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>
+          <when value="indels">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>
+          <when value="custom">
+              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>
+        </conditional>
+    </repeat>
+    
+    <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;">
+      <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
+      <options from_data_table="gatk2_annotations">
+        <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
+        <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
+      </options>
+    </param>
+    
+    <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
+      <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+    </repeat>
+    
+    <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
+        <option value="SNP" selected="True">SNP</option>
+        <option value="INDEL">INDEL</option>
+        <option value="BOTH">BOTH</option>
+    </param>
+    
+    <expand macro="gatk_param_type_conditional" />
+    
+    <expand macro="analysis_type_conditional">
+        <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;"/>
+        <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;"/>
+        <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;"/>
+        <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;"/>
+        <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;"/>
+        <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &amp;lt;shrinkage&amp;gt;"/>
+        <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &amp;lt;dirichlet&amp;gt;"/>
+        <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;"/>
+        <conditional name="bad_variant_selector">
+          <param name="bad_variant_selector_type" type="select" label="How to specify bad variants">
+            <option value="percent" selected="True">Percent</option>
+            <option value="min_num">Number</option>
+          </param>
+          <when value="percent">
+            <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;"/>
+          </when>
+          <when value="min_num">
+            <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;"/>
+          </when>
+        </conditional>
+        <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;"/>
+        <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;"/>
+        <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &amp;lt;ignore_filter&amp;gt;">
+          <conditional name="ignore_filter_type">
+            <param name="ignore_filter_type_selector" type="select" label="Filter Type">
+              <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
+              <option value="LowQual" >LowQual</option>
+              <option value="custom" selected="True">Other</option>
+            </param>
+            <when value="custom">
+              <param name="filter_name" type="text" value="" label="Filter name"/>
+            </when>
+            <when value="HARD_TO_VALIDATE" />
+            <when value="LowQual" />
+          </conditional>
+        </repeat>
+        <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;"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" />
+    <data format="gatk_tranche" name="output_tranches" label="${tool.name} on ${on_string} (Tranches File)" />
+    <data format="txt" name="output_rscript" label="${tool.name} on ${on_string} (RScript File)" />
+    <data format="pdf" name="output_tranches_pdf" label="${tool.name} on ${on_string} (PDF File)" />
+    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <tests>
+      <!-- ADD TESTS -->
+  </tests>
+  <help>
+**What it does**
+
+Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score
+
+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;`_.
+
+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;`_.
+
+If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
+
+------
+
+**Inputs**
+
+GenomeAnalysisTK: VariantRecalibrator accepts a variant input file.
+
+
+**Outputs**
+
+The output is in VCF format.
+
+
+Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
+
+-------
+
+**Settings**::
+
+
+ tranches_file         The output tranches file used by ApplyRecalibration
+ use_annotation        The names of the annotations which should used for calculations
+ 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)
+ maxGaussians          The maximum number of Gaussians to try during variational Bayes algorithm
+ maxIterations         The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.
+ numKMeans             The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.
+ 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.
+ qualThreshold         If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model.
+ shrinkage             The shrinkage parameter in variational Bayes algorithm.
+ dirichlet             The dirichlet parameter in variational Bayes algorithm.
+ priorCounts           The number of prior counts to use in variational Bayes algorithm.
+ 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.
+ 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.
+ recal_file            The output recal file used by ApplyRecalibration
+ 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!
+ 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)
+ ignore_filter         If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file
+ 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
+ rscript_file          The output rscript file generated by the VQSR to aid in visualization of the input data and learned model
+ path_to_resources     Path to resources folder holding the Sting R scripts.
+ ts_filter_level       The truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots
+
+@CITATION_SECTION@
+  </help>
+</tool>