annotate base_recalibrator.xml @ 16:d56503a12975 draft

base_recalibrator out_puts gatk_report
author Jim Johnson <jj@umn.edu>
date Thu, 15 Nov 2012 10:18:27 -0600 (2012-11-15)
parents 74c05070a3f8
children 7533db8dfb5b
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1 <tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.4">
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2 <description>on BAM files</description>
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3 <requirements>
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4 <requirement type="package" version="2.2">gatk</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <command interpreter="python">gatk2_wrapper.py
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8 --max_jvm_heap_fraction "1"
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9 --stdout "${output_log}"
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10 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
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11 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
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12 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
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13 #end if
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14 -p 'java
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15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
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16 -T "BaseRecalibrator"
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17 \$GATK2_SITE_OPTIONS
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18 ##--num_threads 4 ##hard coded, for now
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19 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
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20 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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21 #if $reference_source.reference_source_selector != "history":
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22 -R "${reference_source.ref_file.fields.path}"
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23 #end if
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24 --out "${output_recal}"
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25 ${standard_covs}
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26 #if str( $covariates ) != "None":
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27 #for $cov in str( $covariates ).split( ',' ):
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28 -cov "${cov}"
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29 #end for
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30 #end if
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31 '
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32
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33 #set $snp_dataset_provided = False
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34 #set $rod_binding_names = dict()
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35 #for $rod_binding in $rod_bind:
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36 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
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37 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
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38 #else
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39 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
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40 #end if
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41 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'dbsnp':
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42 #set $snp_dataset_provided = True
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43 #end if
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44 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
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45 -d "--knownSites:${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]}"
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46 #end for
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47
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48 ##start standard gatk options
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49 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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50 #for $pedigree in $gatk_param_type.pedigree:
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51 -p '--pedigree "${pedigree.pedigree_file}"'
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52 #end for
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53 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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54 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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55 #end for
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56 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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57 #for $read_filter in $gatk_param_type.read_filter:
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58 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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59 ###raise Exception( str( dir( $read_filter ) ) )
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60 #for $name, $param in $read_filter.read_filter_type.iteritems():
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61 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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62 #if hasattr( $param.input, 'truevalue' ):
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63 ${param}
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64 #else:
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65 --${name} "${param}"
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66 #end if
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67 #end if
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68 #end for
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69 '
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70 #end for
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71 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
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72 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
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73 #end for
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74
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75 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
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76 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
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77 #end for
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78
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79 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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80
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81 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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82 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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83 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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84 #end if
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85 -p '
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86 --baq "${gatk_param_type.baq}"
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87 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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88 ${gatk_param_type.use_original_qualities}
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89 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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90 --validation_strictness "${gatk_param_type.validation_strictness}"
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91 --interval_merging "${gatk_param_type.interval_merging}"
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92 ${gatk_param_type.disable_experimental_low_memory_sharding}
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93 ${gatk_param_type.non_deterministic_random_seed}
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94 '
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95 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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96 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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97 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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98 #else
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99 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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100 #end if
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101 #end for
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102 #end if
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103
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104 #if str( $reference_source.reference_source_selector ) == "history":
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105 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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106 #end if
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107 ##end standard gatk options
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108
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109 ##start analysis specific options
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110 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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111 -p '
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112 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
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113 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
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114 #end if
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115 #if str( $analysis_param_type.default_platform ) != "default":
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116 --default_platform "${analysis_param_type.default_platform}"
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117 #end if
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118 #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
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119 --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
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120 #end if
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121 #if str( $analysis_param_type.force_platform ) != "default":
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122 --force_platform "${analysis_param_type.force_platform}"
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123 #end if
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124 ${analysis_param_type.exception_if_no_tile}
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125 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
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126 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
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127 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
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128 #end if
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129 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
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130 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
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131 #end if
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132 #end if
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133 --window_size_nqs "${analysis_param_type.window_size_nqs}"
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134 --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
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135 '
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136 #end if
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137 #if not $snp_dataset_provided:
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138 -p '--run_without_dbsnp_potentially_ruining_quality'
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139 #end if
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140 </command>
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141 <inputs>
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142 <conditional name="reference_source">
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143 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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144 <option value="cached">Locally cached</option>
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145 <option value="history">History</option>
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146 </param>
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147 <when value="cached">
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148 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
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149 <validator type="unspecified_build" />
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150 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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151 </param>
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152 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
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153 <options from_data_table="gatk2_picard_indexes">
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154 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
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155 </options>
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156 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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157 </param>
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158 </when>
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159 <when value="history">
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160 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
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161 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
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162 <options>
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163 <filter type="data_meta" key="dbkey" ref="input_bam" />
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164 </options>
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165 </param>
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166 </when>
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167 </conditional>
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168 <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" help="-standard,--standard_covs" />
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169 <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
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170 <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
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171 <option value="ReadGroupCovariate" />
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172 <option value="QualityScoreCovariate" />
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173 <option value="CycleCovariate" />
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174 <option value="DinucCovariate" />
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jjohnson
parents:
diff changeset
175 <!-- covariates below were pulled from list option -->
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jjohnson
parents:
diff changeset
176 <option value="HomopolymerCovariate" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
177 <option value="GCContentCovariate" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
178 <option value="MappingQualityCovariate" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
179 <option value="MinimumNQSCovariate" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
180 <option value="PositionCovariate" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
181 <option value="PrimerRoundCovariate" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
182 <option value="TileCovariate" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
183 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
184
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
185 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-knownSites,--knownSites &amp;lt;knownSites&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
186 <conditional name="rod_bind_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
187 <param name="rod_bind_type_selector" type="select" label="Binding Type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
188 <option value="dbsnp" selected="True">dbSNP</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
189 <option value="snps">SNPs</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
190 <option value="indels">INDELs</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
191 <option value="mask">Mask</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
192 <option value="custom">Custom</option>
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jjohnson
parents:
diff changeset
193 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
194 <when value="dbsnp">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
195 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
196 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
197 <when value="snps">
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jjohnson
parents:
diff changeset
198 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
199 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
200 <when value="indels">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
201 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
202 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
203 <when value="mask">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
204 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
205 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
206 <when value="custom">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
207 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
208 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
209 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
210 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
211 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
212
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
213 <conditional name="gatk_param_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
214 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
215 <option value="basic" selected="True">Basic</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
216 <option value="advanced">Advanced</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
217 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
218 <when value="basic">
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jjohnson
parents:
diff changeset
219 <!-- Do nothing here -->
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jjohnson
parents:
diff changeset
220 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
221 <when value="advanced">
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jjohnson
parents:
diff changeset
222 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
223 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
224 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
225 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
226 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
227 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
228 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
229 <option value="STRICT" selected="True">STRICT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
230 <option value="SILENT">SILENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
231 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
232 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
233 <conditional name="read_filter_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
234 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
235 <option value="BadCigar">BadCigar</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
236 <option value="BadMate">BadMate</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
237 <option value="DuplicateRead">DuplicateRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
238 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
239 <option value="MalformedRead">MalformedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
240 <option value="MappingQuality">MappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
241 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
242 <option value="MappingQualityZero">MappingQualityZero</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
243 <option value="MateSameStrand">MateSameStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
244 <option value="MaxInsertSize">MaxInsertSize</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
245 <option value="MaxReadLength" selected="True">MaxReadLength</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
246 <option value="MissingReadGroup">MissingReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
247 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
248 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
249 <option value="Platform454">Platform454</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
250 <option value="Platform">Platform</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
251 <option value="PlatformUnit">PlatformUnit</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
252 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
253 <option value="ReadName">ReadName</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
254 <option value="ReadStrand">ReadStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
255 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
256 <option value="Sample">Sample</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
257 <option value="SingleReadGroup">SingleReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
258 <option value="UnmappedRead">UnmappedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
259 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
260 <when value="BadCigar">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
261 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
262 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
263 <when value="BadMate">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
264 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
265 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
266 <when value="DuplicateRead">
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jjohnson
parents:
diff changeset
267 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
268 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
269 <when value="FailsVendorQualityCheck">
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jjohnson
parents:
diff changeset
270 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
271 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
272 <when value="MalformedRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
273 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
274 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
275 <when value="MappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
276 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
277 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
278 <when value="MappingQualityUnavailable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
279 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
280 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
281 <when value="MappingQualityZero">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
282 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
283 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
284 <when value="MateSameStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
285 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
286 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
287 <when value="MaxInsertSize">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
288 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
289 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
290 <when value="MaxReadLength">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
291 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
292 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
293 <when value="MissingReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
294 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
295 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
296 <when value="NoOriginalQualityScores">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
297 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
298 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
299 <when value="NotPrimaryAlignment">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
300 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
301 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
302 <when value="Platform454">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
303 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
304 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
305 <when value="Platform">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
306 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
307 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
308 <when value="PlatformUnit">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
309 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
310 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
311 <when value="ReadGroupBlackList">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
312 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
313 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
314 <when value="ReadName">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
315 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
316 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
317 <when value="ReadStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
318 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
319 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
320 <when value="ReassignMappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
321 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
322 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
323 <when value="Sample">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
324 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
325 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
326 <when value="SingleReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
327 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
328 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
329 <when value="UnmappedRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
330 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
331 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
332 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
333 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
334 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
335 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
336 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
337 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
338 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
339 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
340
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
341 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
342 <option value="UNION" selected="True">UNION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
343 <option value="INTERSECTION">INTERSECTION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
344 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
345
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
346 <conditional name="downsampling_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
347 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
348 <option value="NONE" selected="True">NONE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
349 <option value="ALL_READS">ALL_READS</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
350 <option value="BY_SAMPLE">BY_SAMPLE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
351 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
352 <when value="NONE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
353 <!-- no more options here -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
354 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
355 <when value="ALL_READS">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
356 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
357 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
358 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
359 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
360 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
361 <when value="downsample_to_fraction">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
362 <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 &amp;lt;downsample_to_fraction&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
363 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
364 <when value="downsample_to_coverage">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
365 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
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jjohnson
parents:
diff changeset
366 </when>
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jjohnson
parents:
diff changeset
367 </conditional>
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jjohnson
parents:
diff changeset
368 </when>
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jjohnson
parents:
diff changeset
369 <when value="BY_SAMPLE">
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jjohnson
parents:
diff changeset
370 <conditional name="downsample_to_type">
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jjohnson
parents:
diff changeset
371 <param name="downsample_to_type_selector" type="select" label="Downsample method">
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jjohnson
parents:
diff changeset
372 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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jjohnson
parents:
diff changeset
373 <option value="downsample_to_coverage">Downsample by Coverage</option>
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jjohnson
parents:
diff changeset
374 </param>
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jjohnson
parents:
diff changeset
375 <when value="downsample_to_fraction">
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jjohnson
parents:
diff changeset
376 <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 &amp;lt;downsample_to_fraction&amp;gt;"/>
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jjohnson
parents:
diff changeset
377 </when>
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jjohnson
parents:
diff changeset
378 <when value="downsample_to_coverage">
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jjohnson
parents:
diff changeset
379 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
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jjohnson
parents:
diff changeset
380 </when>
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jjohnson
parents:
diff changeset
381 </conditional>
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jjohnson
parents:
diff changeset
382 </when>
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jjohnson
parents:
diff changeset
383 </conditional>
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jjohnson
parents:
diff changeset
384 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
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jjohnson
parents:
diff changeset
385 <option value="OFF" selected="True">OFF</option>
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jjohnson
parents:
diff changeset
386 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
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jjohnson
parents:
diff changeset
387 <option value="RECALCULATE">RECALCULATE</option>
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jjohnson
parents:
diff changeset
388 </param>
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jjohnson
parents:
diff changeset
389 <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 &amp;lt;baqGapOpenPenalty&amp;gt;" />
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jjohnson
parents:
diff changeset
390 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
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jjohnson
parents:
diff changeset
391 <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 &amp;lt;defaultBaseQualities&amp;gt;"/>
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jjohnson
parents:
diff changeset
392 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
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jjohnson
parents:
diff changeset
393 <option value="STRICT" selected="True">STRICT</option>
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jjohnson
parents:
diff changeset
394 <option value="LENIENT">LENIENT</option>
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jjohnson
parents:
diff changeset
395 <option value="SILENT">SILENT</option>
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jjohnson
parents:
diff changeset
396 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
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jjohnson
parents:
diff changeset
397 </param>
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jjohnson
parents:
diff changeset
398 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
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jjohnson
parents:
diff changeset
399 <option value="ALL" selected="True">ALL</option>
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jjohnson
parents:
diff changeset
400 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
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jjohnson
parents:
diff changeset
401 </param>
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jjohnson
parents:
diff changeset
402
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jjohnson
parents:
diff changeset
403 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
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jjohnson
parents:
diff changeset
404 <conditional name="read_group_black_list_type">
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jjohnson
parents:
diff changeset
405 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
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jjohnson
parents:
diff changeset
406 <option value="file" selected="True">Filters in file</option>
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jjohnson
parents:
diff changeset
407 <option value="text">Specify filters as a string</option>
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jjohnson
parents:
diff changeset
408 </param>
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jjohnson
parents:
diff changeset
409 <when value="file">
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jjohnson
parents:
diff changeset
410 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
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jjohnson
parents:
diff changeset
411 </when>
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jjohnson
parents:
diff changeset
412 <when value="text">
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jjohnson
parents:
diff changeset
413 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
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jjohnson
parents:
diff changeset
414 </when>
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jjohnson
parents:
diff changeset
415 </conditional>
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jjohnson
parents:
diff changeset
416 </repeat>
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jjohnson
parents:
diff changeset
417
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jjohnson
parents:
diff changeset
418 <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"/>
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jjohnson
parents:
diff changeset
419 <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"/>
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jjohnson
parents:
diff changeset
420
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jjohnson
parents:
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421 </when>
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jjohnson
parents:
diff changeset
422 </conditional>
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jjohnson
parents:
diff changeset
423
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jjohnson
parents:
diff changeset
424 <conditional name="analysis_param_type">
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jjohnson
parents:
diff changeset
425 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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jjohnson
parents:
diff changeset
426 <option value="basic" selected="True">Basic</option>
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jjohnson
parents:
diff changeset
427 <option value="advanced">Advanced</option>
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jjohnson
parents:
diff changeset
428 </param>
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jjohnson
parents:
diff changeset
429 <when value="basic">
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jjohnson
parents:
diff changeset
430 <!-- Do nothing here -->
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jjohnson
parents:
diff changeset
431 </when>
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jjohnson
parents:
diff changeset
432 <when value="advanced">
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jjohnson
parents:
diff changeset
433 <conditional name="default_read_group_type">
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jjohnson
parents:
diff changeset
434 <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
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jjohnson
parents:
diff changeset
435 <option value="default" selected="True">Don't Set</option>
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jjohnson
parents:
diff changeset
436 <option value="set">Set</option>
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jjohnson
parents:
diff changeset
437 </param>
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jjohnson
parents:
diff changeset
438 <when value="default">
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jjohnson
parents:
diff changeset
439 <!-- do nothing here -->
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jjohnson
parents:
diff changeset
440 </when>
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jjohnson
parents:
diff changeset
441 <when value="set">
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jjohnson
parents:
diff changeset
442 <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
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jjohnson
parents:
diff changeset
443 </when>
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jjohnson
parents:
diff changeset
444 </conditional>
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jjohnson
parents:
diff changeset
445 <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
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jjohnson
parents:
diff changeset
446 <option value="default" selected="True">Don't Set</option>
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jjohnson
parents:
diff changeset
447 <option value="illumina">illumina</option>
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jjohnson
parents:
diff changeset
448 <option value="454">454</option>
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jjohnson
parents:
diff changeset
449 <option value="solid">solid</option>
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jjohnson
parents:
diff changeset
450 </param>
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jjohnson
parents:
diff changeset
451 <conditional name="force_read_group_type">
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jjohnson
parents:
diff changeset
452 <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
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jjohnson
parents:
diff changeset
453 <option value="default" selected="True">Don't Force</option>
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jjohnson
parents:
diff changeset
454 <option value="set">Force</option>
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jjohnson
parents:
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455 </param>
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jjohnson
parents:
diff changeset
456 <when value="default">
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jjohnson
parents:
diff changeset
457 <!-- do nothing here -->
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jjohnson
parents:
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458 </when>
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jjohnson
parents:
diff changeset
459 <when value="set">
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jjohnson
parents:
diff changeset
460 <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
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jjohnson
parents:
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461 </when>
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jjohnson
parents:
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462 </conditional>
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jjohnson
parents:
diff changeset
463 <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
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jjohnson
parents:
diff changeset
464 <option value="default" selected="True">Don't Force</option>
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jjohnson
parents:
diff changeset
465 <option value="illumina">illumina</option>
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jjohnson
parents:
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466 <option value="454">454</option>
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jjohnson
parents:
diff changeset
467 <option value="solid">solid</option>
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jjohnson
parents:
diff changeset
468 </param>
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jjohnson
parents:
diff changeset
469 <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
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jjohnson
parents:
diff changeset
470 <conditional name="solid_options_type">
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jjohnson
parents:
diff changeset
471 <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
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jjohnson
parents:
diff changeset
472 <option value="default" selected="True">Don't Set</option>
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jjohnson
parents:
diff changeset
473 <option value="set">Set</option>
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jjohnson
parents:
diff changeset
474 </param>
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jjohnson
parents:
diff changeset
475 <when value="default">
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jjohnson
parents:
diff changeset
476 <!-- do nothing here -->
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jjohnson
parents:
diff changeset
477 </when>
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jjohnson
parents:
diff changeset
478 <when value="set">
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jjohnson
parents:
diff changeset
479 <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
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jjohnson
parents:
diff changeset
480 <option value="default" selected="True">Don't set</option>
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jjohnson
parents:
diff changeset
481 <option value="DO_NOTHING">DO_NOTHING</option>
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jjohnson
parents:
diff changeset
482 <option value="SET_Q_ZERO">SET_Q_ZERO</option>
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jjohnson
parents:
diff changeset
483 <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
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jjohnson
parents:
diff changeset
484 <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
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jjohnson
parents:
diff changeset
485 </param>
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jjohnson
parents:
diff changeset
486 <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
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jjohnson
parents:
diff changeset
487 <option value="default" selected="True">Don't set</option>
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jjohnson
parents:
diff changeset
488 <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
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jjohnson
parents:
diff changeset
489 <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
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jjohnson
parents:
diff changeset
490 <option value="PURGE_READ">PURGE_READ</option>
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jjohnson
parents:
diff changeset
491 </param>
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jjohnson
parents:
diff changeset
492 </when>
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jjohnson
parents:
diff changeset
493 </conditional>
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jjohnson
parents:
diff changeset
494 <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="window_size_nqs"/>
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jjohnson
parents:
diff changeset
495 <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
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jjohnson
parents:
diff changeset
496 </when>
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jjohnson
parents:
diff changeset
497 </conditional>
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jjohnson
parents:
diff changeset
498 </inputs>
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jjohnson
parents:
diff changeset
499 <outputs>
16
d56503a12975 base_recalibrator out_puts gatk_report
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
500 <data format="gatk_report" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
0
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jjohnson
parents:
diff changeset
501 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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jjohnson
parents:
diff changeset
502 </outputs>
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jjohnson
parents:
diff changeset
503 <tests>
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jjohnson
parents:
diff changeset
504 <test>
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jjohnson
parents:
diff changeset
505 <param name="reference_source_selector" value="history" />
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jjohnson
parents:
diff changeset
506 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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jjohnson
parents:
diff changeset
507 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
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jjohnson
parents:
diff changeset
508 <param name="rod_bind_type_selector" value="dbsnp" />
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jjohnson
parents:
diff changeset
509 <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
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jjohnson
parents:
diff changeset
510 <param name="standard_covs" value="True" />
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jjohnson
parents:
diff changeset
511 <param name="covariates" value="ReadGroupCovariate,HomopolymerCovariate,MinimumNQSCovariate,PositionCovariate" />
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jjohnson
parents:
diff changeset
512 <param name="gatk_param_type_selector" value="basic" />
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jjohnson
parents:
diff changeset
513 <param name="analysis_param_type_selector" value="basic" />
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jjohnson
parents:
diff changeset
514 <output name="output_recal" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" />
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jjohnson
parents:
diff changeset
515 <output name="output_log" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains" compare="contains" />
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jjohnson
parents:
diff changeset
516 </test>
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jjohnson
parents:
diff changeset
517 </tests>
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jjohnson
parents:
diff changeset
518 <help>
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jjohnson
parents:
diff changeset
519 .. class:: warningmark
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jjohnson
parents:
diff changeset
520
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jjohnson
parents:
diff changeset
521 "This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation."
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jjohnson
parents:
diff changeset
522 However, if you do not provide this file, the '--run_without_dbsnp_potentially_ruining_quality' flag will be automatically used, and the command will be allowed to run.
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jjohnson
parents:
diff changeset
523
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jjohnson
parents:
diff changeset
524 **What it does**
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jjohnson
parents:
diff changeset
525
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jjohnson
parents:
diff changeset
526 This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal operating only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors and indicative of poor base quality. This walker generates tables based on various user-specified covariates (such as read group, reported quality score, cycle, and dinucleotide) Since there is a large amount of data one can then calculate an empirical probability of error given the particular covariates seen at this site, where p(error) = num mismatches / num observations The output file is a CSV list of (the several covariate values, num observations, num mismatches, empirical quality score) The first non-comment line of the output file gives the name of the covariates that were used for this calculation. Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added for the user regardless of whether or not they were specified Note: This walker is designed to be used in conjunction with TableRecalibrationWalker.
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jjohnson
parents:
diff changeset
527
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jjohnson
parents:
diff changeset
528 For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_BaseRecalibrator.html&gt;`_.
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jjohnson
parents:
diff changeset
529
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jjohnson
parents:
diff changeset
530 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;`_.
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jjohnson
parents:
diff changeset
531
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jjohnson
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532 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
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533
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534 ------
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535
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536 **Inputs**
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537
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538 GenomeAnalysisTK: BaseRecalibrator accepts an aligned BAM input file.
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539
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540
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541 **Outputs**
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542
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543 The output is in CSV format.
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544
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545
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546 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
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547
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548 -------
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549
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550 **Settings**::
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551
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552
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553 default_read_group If a read has no read group then default to the provided String.
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554 default_platform If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.
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555 force_read_group If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.
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556 force_platform If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.
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557 window_size_nqs The window size used by MinimumNQSCovariate for its calculation
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558 homopolymer_nback The number of previous bases to look at in HomopolymerCovariate
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559 exception_if_no_tile If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
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560 solid_recal_mode How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
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561 solid_nocall_strategy Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
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562 recal_file Filename for the input covariates table recalibration .csv file
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563 out The output CSV file
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564 standard_covs Use the standard set of covariates in addition to the ones listed using the -cov argument
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565 run_without_dbsnp_potentially_ruining_quality If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.
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566
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567 ------
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568
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569 **Citation**
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570
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571 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_
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572
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573 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20644199&gt;`_
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574
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575 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20069535&gt;`_
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576
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577 </help>
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578 </tool>