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1 <tool id="gatk_count_covariates" name="Count Covariates" version="0.0.1">
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2 <description>on BAM files</description>
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3 <command interpreter="python">gatk_wrapper.py
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4 --stdout "${output_log}"
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5 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
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6 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
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7 -p 'java
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8 -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
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9 -T "CountCovariates"
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10 --num_threads 4 ##hard coded, for now
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11 -et "NO_ET" ##ET no phone home
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12 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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13 #if $reference_source.reference_source_selector != "history":
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14 -R "${reference_source.ref_file.fields.path}"
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15 #end if
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16 --recal_file "${output_recal}"
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17 ${standard_covs}
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18 #if $covariates.value:
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19 #for $cov in $covariates.value:
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20 -cov "${cov}"
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21 #end for
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22 #end if
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23 '
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24
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25 #set $snp_dataset_provided = False
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26 #if str( $input_dbsnp_rod ) != "None":
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27 -d "-D" "${input_dbsnp_rod}" "${input_dbsnp_rod.ext}" "dbsnp_rod"
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28 #set $snp_dataset_provided = True
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29 #end if
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30 #set $rod_binding_names = dict()
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31 #for $rod_binding in $rod_bind:
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32 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
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33 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
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34 #else
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35 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
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36 #end if
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37 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'snps':
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38 #set $snp_dataset_provided = True
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39 #end if
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40 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
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41 -d "-B:${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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42 #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
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43 -p '--rodToIntervalTrackName "${rod_bind_name}"'
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44 #end if
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45 #end for
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46
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47 ##start standard gatk options
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48 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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49 #for $sample_metadata in $gatk_param_type.sample_metadata:
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50 -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
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51 #end for
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52 #for $read_filter in $gatk_param_type.read_filter:
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53 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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54 ###raise Exception( str( dir( $read_filter ) ) )
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55 #for $name, $param in $read_filter.read_filter_type.iteritems():
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56 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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57 --${name} "${param}"
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58 #end if
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59 #end for
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60 '
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61 #end for
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62 #if str( $gatk_param_type.input_intervals ) != "None":
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63 -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
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64 #end if
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65 #if str( $gatk_param_type.input_exclude_intervals ) != "None":
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66 -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
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67 #end if
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68
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69 -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
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70 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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71 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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72 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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73 #end if
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74 -p '
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75 --baq "${gatk_param_type.baq}"
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76 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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77 ${gatk_param_type.use_original_qualities}
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78 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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79 --validation_strictness "${gatk_param_type.validation_strictness}"
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80 --interval_merging "${gatk_param_type.interval_merging}"
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81 '
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82 #if str( $gatk_param_type.read_group_black_list ) != "None":
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83 -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
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84 #end if
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85 #end if
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86 #if str( $reference_source.reference_source_selector ) == "history":
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87 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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88 #end if
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89 ##end standard gatk options
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90
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91 ##start analysis specific options
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92 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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93 -p '
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94 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
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95 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
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96 #end if
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97 #if str( $analysis_param_type.default_platform ) != "default":
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98 --default_platform "${analysis_param_type.default_platform}"
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99 #end if
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100 #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
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101 --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
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102 #end if
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103 #if str( $analysis_param_type.force_platform ) != "default":
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104 --force_platform "${analysis_param_type.force_platform}"
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105 #end if
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106 ${analysis_param_type.exception_if_no_tile}
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107 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
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108 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
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109 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
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110 #end if
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111 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
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112 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
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113 #end if
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114 #end if
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115 --window_size_nqs "${analysis_param_type.window_size_nqs}"
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116 --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
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117 '
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118 #end if
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119 #if not $snp_dataset_provided:
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120 -p '--run_without_dbsnp_potentially_ruining_quality'
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121 #end if
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122 </command>
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123 <inputs>
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124 <conditional name="reference_source">
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125 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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126 <option value="cached">Locally cached</option>
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127 <option value="history">History</option>
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128 </param>
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129 <when value="cached">
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130 <param name="input_bam" type="data" format="bam" label="BAM file">
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131 <validator type="unspecified_build" />
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132 <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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133 </param>
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134 <param name="ref_file" type="select" label="Using reference genome">
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135 <options from_data_table="picard_indexes">
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136 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
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137 </options>
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138 </param>
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139 </when>
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140 <when value="history"> <!-- FIX ME!!!! -->
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141 <param name="input_bam" type="data" format="bam" label="BAM file" />
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142 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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143 </when>
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144 </conditional>
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145 <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" />
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146 <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" >
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147 <!-- 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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148 <option value="ReadGroupCovariate" />
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149 <option value="QualityScoreCovariate" />
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150 <option value="CycleCovariate" />
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151 <option value="DinucCovariate" />
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152 <!-- covariates below were pull from source code, since the list option doesn't seem to work (when tried) -->
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153 <option value="HomopolymerCovariate" />
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154 <option value="MappingQualityCovariate" />
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155 <option value="MinimumNQSCovariate" />
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156 <option value="PositionCovariate" />
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157 <option value="PrimerRoundCovariate" />
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158 <option value="TileCovariate" />
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159 </param>
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160 <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" />
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161 <repeat name="rod_bind" title="Binding for reference-ordered data">
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162 <conditional name="rod_bind_type">
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163 <param name="rod_bind_type_selector" type="select" label="Binding Type">
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164 <option value="snps" selected="True">SNPs</option>
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165 <option value="indels">INDELs</option>
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166 <option value="mask">Mask</option>
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167 <option value="custom">Custom</option>
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168 </param>
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169 <when value="snps">
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170 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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171 <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
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172 </when>
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173 <when value="indels">
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174 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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175 <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
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176 </when>
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177 <when value="custom">
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178 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
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179 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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180 <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
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181 </when>
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182 </conditional>
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183 </repeat>
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184
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185 <conditional name="gatk_param_type">
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186 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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187 <option value="basic" selected="True">Basic</option>
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188 <option value="advanced">Advanced</option>
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189 </param>
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190 <when value="basic">
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191 <!-- Do nothing here -->
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192 </when>
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193 <when value="advanced">
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194 <repeat name="sample_metadata" title="Sample Metadata">
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195 <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
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196 </repeat>
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197 <repeat name="read_filter" title="Read Filter">
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198 <conditional name="read_filter_type">
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199 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
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200 <option value="MaxReadLength" selected="True">MaxReadLength</option>
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201 <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
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202 </param>
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203 <when value="ZeroMappingQualityRead">
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204 <!-- no extra options -->
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205 </when>
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206 <when value="MaxReadLength">
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207 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
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208 </when>
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209 </conditional>
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210 </repeat>
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211 <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
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212 <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
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213 <param name="BTI_merge_rule" type="select" label="BTI merge rule">
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214 <option value="UNION" selected="True">UNION</option>
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215 <option value="INTERSECTION">INTERSECTION</option>
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216 </param>
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217 <conditional name="downsampling_type">
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218 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
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219 <option value="NONE" selected="True">NONE</option>
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220 <option value="ALL_READS">ALL_READS</option>
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221 <option value="BY_SAMPLE">BY_SAMPLE</option>
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222 </param>
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223 <when value="NONE">
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224 <!-- no more options here -->
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225 </when>
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226 <when value="ALL_READS">
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227 <conditional name="downsample_to_type">
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228 <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
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229 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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230 <option value="downsample_to_coverage">Downsample by Coverage</option>
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231 </param>
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232 <when value="downsample_to_fraction">
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233 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
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234 </when>
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235 <when value="downsample_to_coverage">
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236 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
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237 </when>
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238 </conditional>
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239 </when>
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240 <when value="BY_SAMPLE">
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241 <conditional name="downsample_to_type">
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242 <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
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243 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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244 <option value="downsample_to_coverage">Downsample by Coverage</option>
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245 </param>
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246 <when value="downsample_to_fraction">
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247 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
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248 </when>
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249 <when value="downsample_to_coverage">
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250 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
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251 </when>
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252 </conditional>
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253 </when>
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254 </conditional>
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255 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
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256 <option value="OFF" selected="True">OFF</option>
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257 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
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258 <option value="RECALCULATE">RECALCULATE</option>
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259 </param>
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260 <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
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261 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
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262 <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
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263 <param name="validation_strictness" type="select" label="How strict should we be with validation">
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264 <option value="STRICT" selected="True">STRICT</option>
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265 <option value="LENIENT">LENIENT</option>
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266 <option value="SILENT">SILENT</option>
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267 </param>
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268 <param name="interval_merging" type="select" label="Interval merging rule">
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269 <option value="ALL" selected="True">ALL</option>
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270 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
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271 </param>
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272 <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
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273 </when>
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274 </conditional>
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275
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276 <conditional name="analysis_param_type">
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277 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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278 <option value="basic" selected="True">Basic</option>
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279 <option value="advanced">Advanced</option>
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280 </param>
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281 <when value="basic">
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282 <!-- Do nothing here -->
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283 </when>
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284 <when value="advanced">
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285 <conditional name="default_read_group_type">
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286 <param name="default_read_group_type_selector" type="select" label="Set default Read Group">
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287 <option value="default" selected="True">Don't Set</option>
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288 <option value="set">Set</option>
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289 </param>
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290 <when value="default">
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291 <!-- do nothing here -->
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292 </when>
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293 <when value="set">
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294 <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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295 </when>
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296 </conditional>
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297 <param name="default_platform" type="select" label="Set default Platform">
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298 <option value="default" selected="True">Don't Set</option>
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299 <option value="illumina">illumina</option>
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300 <option value="454">454</option>
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301 <option value="solid">solid</option>
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302 </param>
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303 <conditional name="force_read_group_type">
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304 <param name="force_read_group_type_selector" type="select" label="Force Read Group">
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305 <option value="default" selected="True">Don't Force</option>
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306 <option value="set">Force</option>
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307 </param>
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308 <when value="default">
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309 <!-- do nothing here -->
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310 </when>
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311 <when value="set">
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312 <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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313 </when>
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314 </conditional>
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315 <param name="force_platform" type="select" label="Force Platform">
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316 <option value="default" selected="True">Don't Force</option>
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317 <option value="illumina">illumina</option>
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318 <option value="454">454</option>
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319 <option value="solid">solid</option>
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320 </param>
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321 <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"/>
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322 <conditional name="solid_options_type">
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323 <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
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324 <option value="default" selected="True">Don't Set</option>
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325 <option value="set">Set</option>
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326 </param>
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327 <when value="default">
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328 <!-- do nothing here -->
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329 </when>
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330 <when value="set">
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331 <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted">
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332 <option value="default" selected="True">Don't set</option>
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333 <option value="DO_NOTHING">DO_NOTHING</option>
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334 <option value="SET_Q_ZERO">SET_Q_ZERO</option>
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335 <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
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336 <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
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337 </param>
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338 <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls">
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339 <option value="default" selected="True">Don't set</option>
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340 <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
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341 <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
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342 <option value="PURGE_READ">PURGE_READ</option>
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343 </param>
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344 </when>
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345 </conditional>
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346 <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/>
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347 <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" />
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348 </when>
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349 </conditional>
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350 </inputs>
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351 <outputs>
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352 <data format="csv" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
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353 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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354 </outputs>
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355 <tests>
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356 <test>
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357 <param name="reference_source_selector" value="history" />
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358 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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359 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
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360 <param name="input_dbsnp_rod" />
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361 <param name="rod_bind_type_selector" value="snps" />
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362 <param name="rodToIntervalTrackName" />
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363 <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
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364 <param name="standard_covs" value="True" />
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365 <param name="covariates" value="ReadGroupCovariate,HomopolymerCovariate,MinimumNQSCovariate,PositionCovariate" />
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366 <param name="gatk_param_type_selector" value="basic" />
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367 <param name="analysis_param_type_selector" value="basic" />
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368 <output name="output_recal" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" />
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369 <output name="output_log" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains" compare="contains" />
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370 </test>
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371 </tests>
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372 <help>
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373 .. class:: warningmark
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374
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375 "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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376 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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377
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378 **What it does**
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379
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380 This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal
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381 operating only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors
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382 and indicative of poor base quality. This walker generates tables based on various user-specified covariates (such
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383 as read group, reported quality score, cycle, and dinucleotide) Since there is a large amount of data one can then
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384 calculate an empirical probability of error given the particular covariates seen at this site, where p(error) = num
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385 mismatches / num observations The output file is a CSV list of (the several covariate values, num observations, num
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386 mismatches, empirical quality score) The first non-comment line of the output file gives the name of the covariates
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387 that were used for this calculation. Note: ReadGroupCovariate and QualityScoreCovariate are required covariates
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388 and will be added for the user regardless of whether or not they were specified Note: This walker is designed to be
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389 used in conjunction with TableRecalibrationWalker.
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390
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391
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392 ------
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393
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394 Please cite the website "http://addlink.here" as well as:
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395
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396 Add citation here 2011.
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397
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398 ------
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399
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400 **Input formats**
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401
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402 GenomeAnalysisTK: CountCovariates accepts an aligned BAM input file.
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403
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404 ------
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405
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406 **Outputs**
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407
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408 The output is in CSV format, see http://addlink.here for more details.
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409
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410 -------
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411
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412 **Settings**::
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413
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414
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415 default_read_group If a read has no read group then default to the provided String.
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416 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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417 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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418 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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419 window_size_nqs The window size used by MinimumNQSCovariate for its calculation
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420 homopolymer_nback The number of previous bases to look at in HomopolymerCovariate
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421 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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422 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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423 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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424 recal_file Filename for the input covariates table recalibration .csv file
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425 out The output CSV file
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426 recal_file Filename for the outputted covariates table recalibration file
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427 standard_covs Use the standard set of covariates in addition to the ones listed using the -cov argument
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428 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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429
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430 </help>
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431 </tool>
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