Mercurial > repos > jjohnson > gatk2
annotate variant_recalibrator.xml @ 31:a5c55503d196 draft
variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 28 Feb 2013 12:44:55 -0600 |
| parents | 6ef8eb568700 |
| children | 76f8ca47b810 |
| rev | line source |
|---|---|
|
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7533db8dfb5b
Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents:
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changeset
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1 <tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="0.0.5"> |
| 0 | 2 <description></description> |
| 3 <requirements> | |
|
18
7533db8dfb5b
Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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4 <requirement type="package" version="2.3">gatk</requirement> |
| 0 | 5 </requirements> |
| 6 <command interpreter="python">gatk2_wrapper.py | |
|
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a5c55503d196
variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set
Jim Johnson <jj@umn.edu>
parents:
28
diff
changeset
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7 #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'UnmappedReadFilter'] |
| 0 | 8 --max_jvm_heap_fraction "1" |
| 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_${var_count}" | |
| 12 #end for | |
| 13 -p 'java | |
| 14 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" | |
| 15 -T "VariantRecalibrator" | |
| 16 \$GATK2_SITE_OPTIONS | |
|
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6ef8eb568700
Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values
Jim Johnson <jj@umn.edu>
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17 \$GATK2_NUM_THREADS |
| 0 | 18 ##--num_threads 4 ##hard coded, for now |
| 19 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file"##ET no phone home | |
| 20 ##-log "${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 ##start standard gatk options | |
| 47 #if $gatk_param_type.gatk_param_type_selector == "advanced": | |
| 48 #for $pedigree in $gatk_param_type.pedigree: | |
| 49 -p '--pedigree "${pedigree.pedigree_file}"' | |
| 50 #end for | |
| 51 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: | |
| 52 -p '--pedigreeString "${pedigree_string.pedigree_string}"' | |
| 53 #end for | |
| 54 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' | |
| 55 #for $read_filter in $gatk_param_type.read_filter: | |
|
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a5c55503d196
variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set
Jim Johnson <jj@umn.edu>
parents:
28
diff
changeset
|
56 -p ' |
|
a5c55503d196
variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set
Jim Johnson <jj@umn.edu>
parents:
28
diff
changeset
|
57 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: |
|
a5c55503d196
variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set
Jim Johnson <jj@umn.edu>
parents:
28
diff
changeset
|
58 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" |
|
a5c55503d196
variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set
Jim Johnson <jj@umn.edu>
parents:
28
diff
changeset
|
59 #end_if |
| 0 | 60 ###raise Exception( str( dir( $read_filter ) ) ) |
| 61 #for $name, $param in $read_filter.read_filter_type.iteritems(): | |
| 62 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: | |
| 63 #if hasattr( $param.input, 'truevalue' ): | |
| 64 ${param} | |
| 65 #else: | |
| 66 --${name} "${param}" | |
| 67 #end if | |
| 68 #end if | |
| 69 #end for | |
| 70 ' | |
| 71 #end for | |
| 72 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): | |
| 73 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" | |
| 74 #end for | |
| 75 | |
| 76 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): | |
| 77 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" | |
| 78 #end for | |
| 79 | |
| 80 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"' | |
| 81 | |
| 82 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' | |
| 83 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": | |
| 84 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' | |
| 85 #end if | |
| 86 -p ' | |
| 87 --baq "${gatk_param_type.baq}" | |
| 88 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}" | |
| 89 ${gatk_param_type.use_original_qualities} | |
| 90 --defaultBaseQualities "${gatk_param_type.default_base_qualities}" | |
| 91 --validation_strictness "${gatk_param_type.validation_strictness}" | |
| 92 --interval_merging "${gatk_param_type.interval_merging}" | |
| 93 ${gatk_param_type.disable_experimental_low_memory_sharding} | |
|
18
7533db8dfb5b
Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
94 ${gatk_param_type.fix_misencoded_quality_scores} |
| 0 | 95 ${gatk_param_type.non_deterministic_random_seed} |
| 96 ' | |
| 97 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): | |
| 98 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": | |
| 99 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" | |
| 100 #else | |
| 101 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' | |
| 102 #end if | |
| 103 #end for | |
| 104 #end if | |
| 105 | |
| 106 #if str( $reference_source.reference_source_selector ) == "history": | |
| 107 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" | |
| 108 #end if | |
| 109 ##end standard gatk options | |
| 110 | |
| 111 ##start analysis specific options | |
| 112 -p ' | |
| 113 #if str( $annotations ) != "None": | |
| 114 #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ): | |
| 115 --use_annotation "${annotation}" | |
| 116 #end for | |
| 117 #end if | |
| 118 #for $additional_annotation in $additional_annotations: | |
| 119 --use_annotation "${additional_annotation.additional_annotation_name}" | |
| 120 #end for | |
| 121 --mode "${mode}" | |
| 122 ' | |
| 123 | |
| 124 #if $analysis_param_type.analysis_param_type_selector == "advanced": | |
| 125 -p ' | |
| 126 --maxGaussians "${analysis_param_type.max_gaussians}" | |
| 127 --maxIterations "${analysis_param_type.max_iterations}" | |
| 128 --numKMeans "${analysis_param_type.num_k_means}" | |
| 129 --stdThreshold "${analysis_param_type.std_threshold}" | |
| 130 --qualThreshold "${analysis_param_type.qual_threshold}" | |
| 131 --shrinkage "${analysis_param_type.shrinkage}" | |
| 132 --dirichlet "${analysis_param_type.dirichlet}" | |
| 133 --priorCounts "${analysis_param_type.prior_counts}" | |
| 134 #if str( $analysis_param_type.bad_variant_selector.bad_variant_selector_type ) == 'percent': | |
| 135 --percentBadVariants "${analysis_param_type.bad_variant_selector.percent_bad_variants}" | |
| 136 #else: | |
| 137 --minNumBadVariants "${analysis_param_type.bad_variant_selector.min_num_bad_variants}" | |
| 138 #end if | |
| 139 --target_titv "${analysis_param_type.target_titv}" | |
| 140 #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ] | |
| 141 --TStranche "${tranche}" | |
| 142 #end for | |
| 143 #for $ignore_filter in $analysis_param_type.ignore_filters: | |
| 144 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector ) | |
| 145 #if $ignore_filter_name == "custom": | |
| 146 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name ) | |
| 147 #end if | |
| 148 --ignore_filter "${ignore_filter_name}" | |
| 149 #end for | |
| 150 --ts_filter_level "${analysis_param_type.ts_filter_level}" | |
| 151 ' | |
| 152 #end if | |
| 153 | |
| 154 | |
| 155 && | |
| 156 mv "${output_rscript}.pdf" "${output_tranches_pdf}" | |
| 157 | |
| 158 </command> | |
| 159 <inputs> | |
| 160 <conditional name="reference_source"> | |
| 161 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> | |
| 162 <option value="cached">Locally cached</option> | |
| 163 <option value="history">History</option> | |
| 164 </param> | |
| 165 <when value="cached"> | |
| 166 <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> | |
| 167 <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /> | |
| 168 </repeat> | |
| 169 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 170 <options from_data_table="gatk_picard_indexes"> | |
| 171 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> | |
| 172 </options> | |
| 173 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 174 </param> | |
| 175 </when> | |
| 176 <when value="history"> <!-- FIX ME!!!! --> | |
| 177 <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> | |
| 178 <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /> | |
| 179 </repeat> | |
| 180 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
| 181 </when> | |
| 182 </conditional> | |
| 183 | |
| 184 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &lt;resource&gt;"> | |
| 185 <conditional name="rod_bind_type"> | |
| 186 <param name="rod_bind_type_selector" type="select" label="Binding Type"> | |
| 187 <option value="dbsnp" selected="True">dbSNP</option> | |
| 188 <option value="variant">Variants</option> | |
| 189 <option value="snps">SNPs</option> | |
| 190 <option value="indels">INDELs</option> | |
| 191 <option value="hapmap">HapMap</option> | |
| 192 <option value="omni">OMNI</option> | |
| 193 <option value="mask">Mask</option> | |
| 194 <option value="custom">Custom</option> | |
| 195 <option value="comp">Comp</option> | |
| 196 </param> | |
| 197 <when value="variant"> | |
| 198 <param name="input_rod" type="data" format="vcf" label="Variant ROD file" /> | |
| 199 <conditional name="rod_training_type"> | |
| 200 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 201 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 202 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 203 </param> | |
| 204 <when value="not_training_truth_known"> | |
| 205 <!-- do nothing here --> | |
| 206 </when> | |
| 207 <when value="is_training_truth_known"> | |
| 208 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 209 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 210 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 211 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 212 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 213 </when> | |
| 214 </conditional> | |
| 215 </when> | |
| 216 <when value="comp"> | |
| 217 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 218 <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/> | |
| 219 <conditional name="rod_training_type"> | |
| 220 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 221 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 222 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 223 </param> | |
| 224 <when value="not_training_truth_known"> | |
| 225 <!-- do nothing here --> | |
| 226 </when> | |
| 227 <when value="is_training_truth_known"> | |
| 228 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 229 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 230 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 231 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 232 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 233 </when> | |
| 234 </conditional> | |
| 235 </when> | |
| 236 <when value="mask"> | |
| 237 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 238 <conditional name="rod_training_type"> | |
| 239 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 240 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 241 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 242 </param> | |
| 243 <when value="not_training_truth_known"> | |
| 244 <!-- do nothing here --> | |
| 245 </when> | |
| 246 <when value="is_training_truth_known"> | |
| 247 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 248 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 249 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 250 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 251 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 252 </when> | |
| 253 </conditional> | |
| 254 </when> | |
| 255 <when value="dbsnp"> | |
| 256 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 257 <conditional name="rod_training_type"> | |
| 258 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 259 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 260 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 261 </param> | |
| 262 <when value="not_training_truth_known"> | |
| 263 <!-- do nothing here --> | |
| 264 </when> | |
| 265 <when value="is_training_truth_known"> | |
| 266 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 267 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 268 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 269 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 270 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 271 </when> | |
| 272 </conditional> | |
| 273 </when> | |
| 274 <when value="snps"> | |
| 275 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 276 <conditional name="rod_training_type"> | |
| 277 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 278 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 279 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 280 </param> | |
| 281 <when value="not_training_truth_known"> | |
| 282 <!-- do nothing here --> | |
| 283 </when> | |
| 284 <when value="is_training_truth_known"> | |
| 285 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 286 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 287 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 288 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 289 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 290 </when> | |
| 291 </conditional> | |
| 292 </when> | |
| 293 <when value="hapmap"> | |
| 294 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 295 <conditional name="rod_training_type"> | |
| 296 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 297 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 298 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 299 </param> | |
| 300 <when value="not_training_truth_known"> | |
| 301 <!-- do nothing here --> | |
| 302 </when> | |
| 303 <when value="is_training_truth_known"> | |
| 304 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 305 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 306 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 307 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 308 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 309 </when> | |
| 310 </conditional> | |
| 311 </when> | |
| 312 <when value="omni"> | |
| 313 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 314 <conditional name="rod_training_type"> | |
| 315 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 316 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 317 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 318 </param> | |
| 319 <when value="not_training_truth_known"> | |
| 320 <!-- do nothing here --> | |
| 321 </when> | |
| 322 <when value="is_training_truth_known"> | |
| 323 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 324 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 325 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 326 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 327 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 328 </when> | |
| 329 </conditional> | |
| 330 </when> | |
| 331 <when value="indels"> | |
| 332 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 333 <conditional name="rod_training_type"> | |
| 334 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 335 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 336 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 337 </param> | |
| 338 <when value="not_training_truth_known"> | |
| 339 <!-- do nothing here --> | |
| 340 </when> | |
| 341 <when value="is_training_truth_known"> | |
| 342 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 343 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 344 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 345 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 346 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 347 </when> | |
| 348 </conditional> | |
| 349 </when> | |
| 350 <when value="custom"> | |
| 351 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> | |
| 352 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 353 <conditional name="rod_training_type"> | |
| 354 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 355 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 356 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 357 </param> | |
| 358 <when value="not_training_truth_known"> | |
| 359 <!-- do nothing here --> | |
| 360 </when> | |
| 361 <when value="is_training_truth_known"> | |
| 362 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 363 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 364 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 365 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 366 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 367 </when> | |
| 368 </conditional> | |
| 369 </when> | |
| 370 </conditional> | |
| 371 </repeat> | |
| 372 | |
| 373 <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &lt;use_annotation&gt;"> | |
| 374 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> | |
| 375 <options from_data_table="gatk2_annotations"> | |
| 376 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> | |
| 377 <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/> | |
| 378 </options> | |
| 379 </param> | |
| 380 | |
| 381 <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &lt;use_annotation&gt;"> | |
| 382 <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> | |
| 383 </repeat> | |
| 384 | |
| 385 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;"> | |
| 386 <option value="SNP" selected="True">SNP</option> | |
| 387 <option value="INDEL">INDEL</option> | |
| 388 <option value="BOTH">BOTH</option> | |
| 389 </param> | |
| 390 | |
| 391 <conditional name="gatk_param_type"> | |
| 392 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> | |
| 393 <option value="basic" selected="True">Basic</option> | |
| 394 <option value="advanced">Advanced</option> | |
| 395 </param> | |
| 396 <when value="basic"> | |
| 397 <!-- Do nothing here --> | |
| 398 </when> | |
| 399 <when value="advanced"> | |
| 400 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"> | |
| 401 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/> | |
| 402 </repeat> | |
| 403 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"> | |
| 404 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/> | |
| 405 </repeat> | |
| 406 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"> | |
| 407 <option value="STRICT" selected="True">STRICT</option> | |
| 408 <option value="SILENT">SILENT</option> | |
| 409 </param> | |
| 410 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"> | |
| 411 <conditional name="read_filter_type"> | |
| 412 <param name="read_filter_type_selector" type="select" label="Read Filter Type"> | |
| 413 <option value="BadCigar">BadCigar</option> | |
| 414 <option value="BadMate">BadMate</option> | |
| 415 <option value="DuplicateRead">DuplicateRead</option> | |
| 416 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> | |
| 417 <option value="MalformedRead">MalformedRead</option> | |
| 418 <option value="MappingQuality">MappingQuality</option> | |
| 419 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> | |
| 420 <option value="MappingQualityZero">MappingQualityZero</option> | |
| 421 <option value="MateSameStrand">MateSameStrand</option> | |
| 422 <option value="MaxInsertSize">MaxInsertSize</option> | |
| 423 <option value="MaxReadLength" selected="True">MaxReadLength</option> | |
| 424 <option value="MissingReadGroup">MissingReadGroup</option> | |
| 425 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> | |
| 426 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> | |
| 427 <option value="Platform454">Platform454</option> | |
| 428 <option value="Platform">Platform</option> | |
| 429 <option value="PlatformUnit">PlatformUnit</option> | |
| 430 <option value="ReadGroupBlackList">ReadGroupBlackList</option> | |
| 431 <option value="ReadName">ReadName</option> | |
| 432 <option value="ReadStrand">ReadStrand</option> | |
| 433 <option value="ReassignMappingQuality">ReassignMappingQuality</option> | |
| 434 <option value="Sample">Sample</option> | |
| 435 <option value="SingleReadGroup">SingleReadGroup</option> | |
| 436 <option value="UnmappedRead">UnmappedRead</option> | |
| 437 </param> | |
| 438 <when value="BadCigar"> | |
| 439 <!-- no extra options --> | |
| 440 </when> | |
| 441 <when value="BadMate"> | |
| 442 <!-- no extra options --> | |
| 443 </when> | |
| 444 <when value="DuplicateRead"> | |
| 445 <!-- no extra options --> | |
| 446 </when> | |
| 447 <when value="FailsVendorQualityCheck"> | |
| 448 <!-- no extra options --> | |
| 449 </when> | |
| 450 <when value="MalformedRead"> | |
| 451 <!-- no extra options --> | |
| 452 </when> | |
| 453 <when value="MappingQuality"> | |
| 454 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> | |
| 455 </when> | |
| 456 <when value="MappingQualityUnavailable"> | |
| 457 <!-- no extra options --> | |
| 458 </when> | |
| 459 <when value="MappingQualityZero"> | |
| 460 <!-- no extra options --> | |
| 461 </when> | |
| 462 <when value="MateSameStrand"> | |
| 463 <!-- no extra options --> | |
| 464 </when> | |
| 465 <when value="MaxInsertSize"> | |
| 466 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> | |
| 467 </when> | |
| 468 <when value="MaxReadLength"> | |
| 469 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> | |
| 470 </when> | |
| 471 <when value="MissingReadGroup"> | |
| 472 <!-- no extra options --> | |
| 473 </when> | |
| 474 <when value="NoOriginalQualityScores"> | |
| 475 <!-- no extra options --> | |
| 476 </when> | |
| 477 <when value="NotPrimaryAlignment"> | |
| 478 <!-- no extra options --> | |
| 479 </when> | |
| 480 <when value="Platform454"> | |
| 481 <!-- no extra options --> | |
| 482 </when> | |
| 483 <when value="Platform"> | |
| 484 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> | |
| 485 </when> | |
| 486 <when value="PlatformUnit"> | |
| 487 <!-- no extra options --> | |
| 488 </when> | |
| 489 <when value="ReadGroupBlackList"> | |
| 490 <!-- no extra options --> | |
| 491 </when> | |
| 492 <when value="ReadName"> | |
| 493 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> | |
| 494 </when> | |
| 495 <when value="ReadStrand"> | |
| 496 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> | |
| 497 </when> | |
| 498 <when value="ReassignMappingQuality"> | |
| 499 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> | |
| 500 </when> | |
| 501 <when value="Sample"> | |
| 502 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> | |
| 503 </when> | |
| 504 <when value="SingleReadGroup"> | |
| 505 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> | |
| 506 </when> | |
| 507 <when value="UnmappedRead"> | |
| 508 <!-- no extra options --> | |
| 509 </when> | |
| 510 </conditional> | |
| 511 </repeat> | |
| 512 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"> | |
| 513 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> | |
| 514 </repeat> | |
| 515 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"> | |
| 516 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> | |
| 517 </repeat> | |
| 518 | |
| 519 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"> | |
| 520 <option value="UNION" selected="True">UNION</option> | |
| 521 <option value="INTERSECTION">INTERSECTION</option> | |
| 522 </param> | |
| 523 | |
| 524 <conditional name="downsampling_type"> | |
| 525 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"> | |
| 526 <option value="NONE" selected="True">NONE</option> | |
| 527 <option value="ALL_READS">ALL_READS</option> | |
| 528 <option value="BY_SAMPLE">BY_SAMPLE</option> | |
| 529 </param> | |
| 530 <when value="NONE"> | |
| 531 <!-- no more options here --> | |
| 532 </when> | |
| 533 <when value="ALL_READS"> | |
| 534 <conditional name="downsample_to_type"> | |
| 535 <param name="downsample_to_type_selector" type="select" label="Downsample method"> | |
| 536 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> | |
| 537 <option value="downsample_to_coverage">Downsample by Coverage</option> | |
| 538 </param> | |
| 539 <when value="downsample_to_fraction"> | |
| 540 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/> | |
| 541 </when> | |
| 542 <when value="downsample_to_coverage"> | |
| 543 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/> | |
| 544 </when> | |
| 545 </conditional> | |
| 546 </when> | |
| 547 <when value="BY_SAMPLE"> | |
| 548 <conditional name="downsample_to_type"> | |
| 549 <param name="downsample_to_type_selector" type="select" label="Downsample method"> | |
| 550 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> | |
| 551 <option value="downsample_to_coverage">Downsample by Coverage</option> | |
| 552 </param> | |
| 553 <when value="downsample_to_fraction"> | |
| 554 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/> | |
| 555 </when> | |
| 556 <when value="downsample_to_coverage"> | |
| 557 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/> | |
| 558 </when> | |
| 559 </conditional> | |
| 560 </when> | |
| 561 </conditional> | |
| 562 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"> | |
| 563 <option value="OFF" selected="True">OFF</option> | |
| 564 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option> | |
| 565 <option value="RECALCULATE">RECALCULATE</option> | |
| 566 </param> | |
| 567 <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /> | |
| 568 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> | |
| 569 <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> | |
| 570 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"> | |
| 571 <option value="STRICT" selected="True">STRICT</option> | |
| 572 <option value="LENIENT">LENIENT</option> | |
| 573 <option value="SILENT">SILENT</option> | |
| 574 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--> | |
| 575 </param> | |
| 576 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"> | |
| 577 <option value="ALL" selected="True">ALL</option> | |
| 578 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option> | |
| 579 </param> | |
| 580 | |
| 581 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"> | |
| 582 <conditional name="read_group_black_list_type"> | |
| 583 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> | |
| 584 <option value="file" selected="True">Filters in file</option> | |
| 585 <option value="text">Specify filters as a string</option> | |
| 586 </param> | |
| 587 <when value="file"> | |
| 588 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> | |
| 589 </when> | |
| 590 <when value="text"> | |
| 591 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> | |
| 592 </when> | |
| 593 </conditional> | |
| 594 </repeat> | |
| 595 | |
| 596 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> | |
| 597 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/> | |
|
18
7533db8dfb5b
Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
598 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/> |
| 0 | 599 |
| 600 </when> | |
| 601 </conditional> | |
| 602 | |
| 603 <conditional name="analysis_param_type"> | |
| 604 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> | |
| 605 <option value="basic" selected="True">Basic</option> | |
| 606 <option value="advanced">Advanced</option> | |
| 607 </param> | |
| 608 <when value="basic"> | |
| 609 <!-- Do nothing here --> | |
| 610 </when> | |
| 611 <when value="advanced"> | |
| 612 <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10" help="-mG,--maxGaussians &lt;maxGaussians&gt;"/> | |
| 613 <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 &lt;maxIterations&gt;"/> | |
| 614 <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 &lt;numKMeans&gt;"/> | |
| 615 <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 &lt;stdThreshold&gt;"/> | |
| 616 <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 &lt;qualThreshold&gt;"/> | |
| 617 <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &lt;shrinkage&gt;"/> | |
| 618 <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &lt;dirichlet&gt;"/> | |
| 619 <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;"/> | |
| 620 <conditional name="bad_variant_selector"> | |
| 621 <param name="bad_variant_selector_type" type="select" label="How to specify bad variants"> | |
| 622 <option value="percent" selected="True">Percent</option> | |
| 623 <option value="min_num">Number</option> | |
| 624 </param> | |
| 625 <when value="percent"> | |
| 626 <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 &lt;percentBadVariants&gt;"/> | |
| 627 </when> | |
| 628 <when value="min_num"> | |
| 629 <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 &lt;minNumBadVariants&gt;"/> | |
| 630 </when> | |
| 631 </conditional> | |
| 632 <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;"/> | |
| 633 <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;"/> | |
| 634 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;"> | |
| 635 <conditional name="ignore_filter_type"> | |
| 636 <param name="ignore_filter_type_selector" type="select" label="Filter Type"> | |
| 637 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> | |
| 638 <option value="LowQual" >LowQual</option> | |
| 639 <option value="custom" selected="True">Other</option> | |
| 640 </param> | |
| 641 <when value="custom"> | |
| 642 <param name="filter_name" type="text" value="" label="Filter name"/> | |
| 643 </when> | |
| 644 <when value="HARD_TO_VALIDATE" /> | |
| 645 <when value="LowQual" /> | |
| 646 </conditional> | |
| 647 </repeat> | |
| 648 <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 &lt;ts_filter_level&gt;"/> | |
| 649 </when> | |
| 650 </conditional> | |
| 651 </inputs> | |
| 652 <outputs> | |
| 653 <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" /> | |
| 654 <data format="gatk_tranche" name="output_tranches" label="${tool.name} on ${on_string} (Tranches File)" /> | |
| 655 <data format="txt" name="output_rscript" label="${tool.name} on ${on_string} (RScript File)" /> | |
| 656 <data format="pdf" name="output_tranches_pdf" label="${tool.name} on ${on_string} (PDF File)" /> | |
| 657 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 658 </outputs> | |
| 659 <tests> | |
| 660 <!-- ADD TESTS --> | |
| 661 </tests> | |
| 662 <help> | |
| 663 **What it does** | |
| 664 | |
| 665 Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score | |
| 666 | |
| 667 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>`_. | |
| 668 | |
| 669 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 670 | |
| 671 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 672 | |
| 673 ------ | |
| 674 | |
| 675 **Inputs** | |
| 676 | |
| 677 GenomeAnalysisTK: VariantRecalibrator accepts a variant input file. | |
| 678 | |
| 679 | |
| 680 **Outputs** | |
| 681 | |
| 682 The output is in VCF format. | |
| 683 | |
| 684 | |
| 685 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 686 | |
| 687 ------- | |
| 688 | |
| 689 **Settings**:: | |
| 690 | |
| 691 | |
| 692 tranches_file The output tranches file used by ApplyRecalibration | |
| 693 use_annotation The names of the annotations which should used for calculations | |
| 694 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) | |
| 695 maxGaussians The maximum number of Gaussians to try during variational Bayes algorithm | |
| 696 maxIterations The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected. | |
| 697 numKMeans The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model. | |
| 698 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. | |
| 699 qualThreshold If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model. | |
| 700 shrinkage The shrinkage parameter in variational Bayes algorithm. | |
| 701 dirichlet The dirichlet parameter in variational Bayes algorithm. | |
| 702 priorCounts The number of prior counts to use in variational Bayes algorithm. | |
| 703 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. | |
| 704 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. | |
| 705 recal_file The output recal file used by ApplyRecalibration | |
| 706 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! | |
| 707 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) | |
| 708 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file | |
| 709 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 | |
| 710 rscript_file The output rscript file generated by the VQSR to aid in visualization of the input data and learned model | |
| 711 path_to_resources Path to resources folder holding the Sting R scripts. | |
| 712 ts_filter_level The truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots | |
| 713 | |
| 714 ------ | |
| 715 | |
| 716 **Citation** | |
| 717 | |
| 718 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ | |
| 719 | |
| 720 Please also site `McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. Epub 2010 Jul 19. <http://www.ncbi.nlm.nih.gov/pubmed/20644199>`_ | |
| 721 | |
| 722 If you use this tool in Galaxy, please cite `Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. <http://www.ncbi.nlm.nih.gov/pubmed/20069535>`_ | |
| 723 | |
| 724 </help> | |
| 725 </tool> |