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1 <tool id="gatk_table_recalibration" name="Table Recalibration" 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 "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
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9 -T "TableRecalibration"
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10 -o "${output_bam}"
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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 "${input_recal}"
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17 --disable_bam_indexing
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18 '
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19 ##start standard gatk options
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20 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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21 #for $sample_metadata in $gatk_param_type.sample_metadata:
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22 -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
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23 #end for
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24 #for $read_filter in $gatk_param_type.read_filter:
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25 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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26 ###raise Exception( str( dir( $read_filter ) ) )
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27 #for $name, $param in $read_filter.read_filter_type.iteritems():
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28 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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29 --${name} "${param}"
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30 #end if
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31 #end for
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32 '
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33 #end for
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34 #if str( $gatk_param_type.input_intervals ) != "None":
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35 -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
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36 #end if
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37 #if str( $gatk_param_type.input_exclude_intervals ) != "None":
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38 -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
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39 #end if
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40 #set $rod_binding_names = dict()
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41 #for $rod_binding in $gatk_param_type.rod_bind:
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42 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
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43 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
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44 #else
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45 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
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46 #end if
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47 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
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48 -d "-B:${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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49 #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
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50 -p '--rodToIntervalTrackName "${rod_bind_name}"'
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51 #end if
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52 #end for
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53 -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
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54 #if str( $gatk_param_type.input_dbsnp_rod ) != "None":
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55 -d "-D" "${gatk_param_type.input_dbsnp_rod}" "${gatk_param_type.input_dbsnp_rod.ext}" "dbsnp_rod"
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56 #end if
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57 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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58 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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59 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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60 #end if
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61 -p '
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62 --baq "${gatk_param_type.baq}"
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63 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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64 ${gatk_param_type.use_original_qualities}
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65 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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66 --validation_strictness "${gatk_param_type.validation_strictness}"
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67 --interval_merging "${gatk_param_type.interval_merging}"
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68 '
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69 #if str( $gatk_param_type.read_group_black_list ) != "None":
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70 -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
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71 #end if
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72 #end if
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73 #if str( $reference_source.reference_source_selector ) == "history":
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74 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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75 #end if
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76 ##end standard gatk options
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77
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78 ##start analysis specific options
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79 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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80 -p '
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81 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
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82 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
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83 #end if
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84 #if str( $analysis_param_type.default_platform ) != "default":
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85 --default_platform "${analysis_param_type.default_platform}"
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86 #end if
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87 #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
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88 --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
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89 #end if
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90 #if str( $analysis_param_type.force_platform ) != "default":
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91 --force_platform "${analysis_param_type.force_platform}"
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92 #end if
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93 ${analysis_param_type.exception_if_no_tile}
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94 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
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95 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
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96 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
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97 #end if
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98 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
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99 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
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100 #end if
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101 #end if
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102 ${analysis_param_type.simplify_bam}
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103 --preserve_qscores_less_than "${analysis_param_type.preserve_qscores_less_than}"
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104 --smoothing "${analysis_param_type.smoothing}"
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105 --max_quality_score "${analysis_param_type.max_quality_score}"
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106 --window_size_nqs "${analysis_param_type.window_size_nqs}"
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107 --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
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108 ${analysis_param_type.do_not_write_original_quals}
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109 '
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110 #end if
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111 </command>
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112 <inputs>
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113 <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" />
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114 <conditional name="reference_source">
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115 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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116 <option value="cached">Locally cached</option>
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117 <option value="history">History</option>
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118 </param>
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119 <when value="cached">
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120 <param name="input_bam" type="data" format="bam" label="BAM file">
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121 <validator type="unspecified_build" />
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122 <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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123 </param>
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124 <param name="ref_file" type="select" label="Using reference genome">
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125 <options from_data_table="picard_indexes">
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126 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
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127 </options>
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128 </param>
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129 </when>
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130 <when value="history"> <!-- FIX ME!!!! -->
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131 <param name="input_bam" type="data" format="bam" label="BAM file" />
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132 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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133 </when>
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134 </conditional>
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135
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136 <conditional name="gatk_param_type">
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137 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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138 <option value="basic" selected="True">Basic</option>
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139 <option value="advanced">Advanced</option>
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140 </param>
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141 <when value="basic">
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142 <!-- Do nothing here -->
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143 </when>
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144 <when value="advanced">
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145 <repeat name="sample_metadata" title="Sample Metadata">
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146 <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
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147 </repeat>
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148 <repeat name="read_filter" title="Read Filter">
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149 <conditional name="read_filter_type">
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150 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
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151 <option value="MaxReadLength" selected="True">MaxReadLength</option>
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152 <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
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153 </param>
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154 <when value="ZeroMappingQualityRead">
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155 <!-- no extra options -->
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156 </when>
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157 <when value="MaxReadLength">
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158 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
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159 </when>
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160 </conditional>
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161 </repeat>
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162 <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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163 <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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164 <repeat name="rod_bind" title="Binding for reference-ordered data">
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165 <conditional name="rod_bind_type">
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166 <param name="rod_bind_type_selector" type="select" label="Binding Type">
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167 <option value="snps" selected="True">SNPs</option>
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168 <option value="indels">INDELs</option>
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169 <option value="custom">Custom</option>
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170 </param>
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171 <when value="snps">
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172 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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173 <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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174 </when>
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175 <when value="indels">
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176 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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177 <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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178 </when>
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179 <when value="custom">
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180 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
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181 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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182 <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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183 </when>
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184 </conditional>
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185 </repeat>
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186 <param name="BTI_merge_rule" type="select" label="BTI merge rule">
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187 <option value="UNION" selected="True">UNION</option>
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188 <option value="INTERSECTION">INTERSECTION</option>
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189 </param>
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190 <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" />
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191 <conditional name="downsampling_type">
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192 <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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193 <option value="NONE" selected="True">NONE</option>
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194 <option value="ALL_READS">ALL_READS</option>
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195 <option value="BY_SAMPLE">BY_SAMPLE</option>
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196 </param>
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197 <when value="NONE">
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198 <!-- no more options here -->
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199 </when>
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200 <when value="ALL_READS">
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201 <conditional name="downsample_to_type">
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202 <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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203 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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204 <option value="downsample_to_coverage">Downsample by Coverage</option>
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205 </param>
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206 <when value="downsample_to_fraction">
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207 <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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208 </when>
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209 <when value="downsample_to_coverage">
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210 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
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211 </when>
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212 </conditional>
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213 </when>
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214 <when value="BY_SAMPLE">
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215 <conditional name="downsample_to_type">
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216 <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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217 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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218 <option value="downsample_to_coverage">Downsample by Coverage</option>
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219 </param>
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220 <when value="downsample_to_fraction">
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221 <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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222 </when>
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223 <when value="downsample_to_coverage">
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224 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
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225 </when>
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226 </conditional>
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227 </when>
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228 </conditional>
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229 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
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230 <option value="OFF" selected="True">OFF</option>
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231 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
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232 <option value="RECALCULATE">RECALCULATE</option>
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233 </param>
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234 <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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235 <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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236 <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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237 <param name="validation_strictness" type="select" label="How strict should we be with validation">
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238 <option value="STRICT" selected="True">STRICT</option>
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239 <option value="LENIENT">LENIENT</option>
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240 <option value="SILENT">SILENT</option>
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241 </param>
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242 <param name="interval_merging" type="select" label="Interval merging rule">
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243 <option value="ALL" selected="True">ALL</option>
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244 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
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245 </param>
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246 <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
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247 </when>
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248 </conditional>
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249
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250
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251 <conditional name="analysis_param_type">
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252 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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253 <option value="basic" selected="True">Basic</option>
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254 <option value="advanced">Advanced</option>
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255 </param>
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256 <when value="basic">
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257 <!-- Do nothing here -->
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258 </when>
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259 <when value="advanced">
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260 <conditional name="default_read_group_type">
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261 <param name="default_read_group_type_selector" type="select" label="Set default Read Group">
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262 <option value="default" selected="True">Don't Set</option>
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263 <option value="set">Set</option>
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264 </param>
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265 <when value="default">
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266 <!-- do nothing here -->
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267 </when>
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268 <when value="set">
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269 <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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270 </when>
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271 </conditional>
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272 <param name="default_platform" type="select" label="Set default Platform">
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273 <option value="default" selected="True">Don't Set</option>
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274 <option value="illumina">illumina</option>
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275 <option value="454">454</option>
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276 <option value="solid">solid</option>
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277 </param>
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278 <conditional name="force_read_group_type">
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279 <param name="force_read_group_type_selector" type="select" label="Force Read Group">
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280 <option value="default" selected="True">Don't Force</option>
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281 <option value="set">Force</option>
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282 </param>
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283 <when value="default">
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284 <!-- do nothing here -->
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285 </when>
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286 <when value="set">
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287 <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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288 </when>
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289 </conditional>
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290 <param name="force_platform" type="select" label="Force Platform">
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291 <option value="default" selected="True">Don't Force</option>
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292 <option value="illumina">illumina</option>
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293 <option value="454">454</option>
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294 <option value="solid">solid</option>
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295 </param>
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296 <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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297 <conditional name="solid_options_type">
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298 <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
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299 <option value="default" selected="True">Don't Set</option>
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300 <option value="set">Set</option>
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301 </param>
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302 <when value="default">
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303 <!-- do nothing here -->
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304 </when>
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305 <when value="set">
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306 <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted">
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307 <option value="default" selected="True">Don't set</option>
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308 <option value="DO_NOTHING">DO_NOTHING</option>
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309 <option value="SET_Q_ZERO">SET_Q_ZERO</option>
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310 <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
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311 <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
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312 </param>
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313 <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls">
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314 <option value="default" selected="True">Don't set</option>
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315 <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
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316 <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
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317 <option value="PURGE_READ">PURGE_READ</option>
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318 </param>
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319 </when>
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320 </conditional>
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321 <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM"/>
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322 <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/>
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323 <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" />
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324 <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated"/>
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325 <param name="smoothing" type="integer" value="1" label="smoothing"/>
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326 <param name="max_quality_score" type="integer" value="50" label="Max quality score"/>
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327 <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag"/>
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328 </when>
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329 </conditional>
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330 </inputs>
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331 <outputs>
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332 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
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333 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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334 </outputs>
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335 <tests>
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336 <test>
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337 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
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338 <param name="reference_source_selector" value="history" />
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339 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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340 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
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341 <param name="gatk_param_type_selector" value="basic" />
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342 <param name="analysis_param_type_selector" value="basic" />
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343 <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="2" />
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344 <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" />
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345 </test>
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346 </tests>
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347 <help>
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348 **What it does**
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349
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350 This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For
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351 each base in each read this walker calculates various user-specified covariates (such as read group, reported
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352 quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical
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353 base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file
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354 with these updated (recalibrated) reads. Note: This walker expects as input the recalibration table file generated
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355 previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with
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356 CovariateCounterWalker.
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357
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358 ------
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359
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360 Please cite the website "http://addlink.here" as well as:
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361
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362 Add citation here 2011.
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363
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364 ------
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365
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366 **Input formats**
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367
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368 GenomeAnalysisTK: TableRecalibration accepts an aligned BAM and a recalibration CSV input files.
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369
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370 ------
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371
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372 **Outputs**
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373
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374 The output is in BAM format, see http://addlink.here for more details.
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375
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376 -------
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377
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378 **Settings**::
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379
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380 default_read_group If a read has no read group then default to the provided String.
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381 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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382 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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383 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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384 window_size_nqs The window size used by MinimumNQSCovariate for its calculation
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385 homopolymer_nback The number of previous bases to look at in HomopolymerCovariate
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386 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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387 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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388 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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389 recal_file Filename for the input covariates table recalibration .csv file
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390 out The output BAM file
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391 bam_compression Compression level to use for writing BAM files
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392 disable_bam_indexing Turn off on-the-fly creation of indices for output BAM files.
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393 simplifyBAM If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier
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394 preserve_qscores_less_than Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases
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395 smoothing Number of imaginary counts to add to each bin bin order to smooth out bins with few data points, default=1
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396 max_quality_score The integer value at which to cap the quality scores, default=50
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397 doNotWriteOriginalQuals If true, we will not write the original quality (OQ) tag for each read
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398
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399 </help>
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400 </tool>
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