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author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 04 Feb 2014 17:26:26 -0500
parents ae6edc0012ba
children d5f866df45ae
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1 <tool id="naive_variant_caller" name="Naive Variant Caller" version="0.0.1">
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2 <description> - tabulate variable sites from BAM datasets</description>
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3 <requirements>
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4 <requirement type="package" version="1.7.1">numpy</requirement>
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5 <requirement type="package" version="0.0.1">pyBamParser</requirement>
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6 <requirement type="package" version="0.0.1">pyBamTools</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" err_level="fatal" />
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10 <exit_code range=":-1" err_level="fatal" />
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11 </stdio>
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12 <command interpreter="python">naive_variant_caller.py
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13 -o "${output_vcf}"
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14
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15 #for $input_bam in $reference_source.input_bams:
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16 -b "${input_bam.input_bam}"
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17 -i "${input_bam.input_bam.metadata.bam_index}"
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18 #end for
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19
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20 #if $reference_source.reference_source_selector != "history":
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21 -r "${reference_source.ref_file.fields.path}"
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22 #elif $reference_source.ref_file:
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23 -r "${reference_source.ref_file}"
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24 #end if
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25
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26 #for $region in $regions:
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27 --region "${region.chromosome}:${region.start}-${region.end}"
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28 #end for
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29
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30 ${variants_only}
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31
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32 ${use_strand}
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33
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34 --ploidy "${$ploidy}"
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35
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36 --min_support_depth "${min_support_depth}"
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37
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38 #if str($min_base_quality):
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39 --min_base_quality "${min_base_quality}"
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40 #end if
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41
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42 #if str($min_mapping_quality):
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43 --min_mapping_quality "${min_mapping_quality}"
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44 #end if
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45
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46 --allow_out_of_bounds_positions
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47
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48 #if str( $advanced_options.advanced_options_selector ) == "advanced":
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49 --coverage_dtype "${advanced_options.coverage_dtype}"
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50 ${advanced_options.safe}
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51 #else
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52 --coverage_dtype "uint64"
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53 #end if
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54 </command>
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55 <inputs>
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56 <conditional name="reference_source">
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57 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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58 <option value="cached">Locally cached</option>
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59 <option value="history">History</option>
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60 </param>
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61 <when value="cached">
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62 <repeat name="input_bams" title="BAM file" min="1" >
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63 <param name="input_bam" type="data" format="bam" label="BAM file">
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64 <validator type="unspecified_build" />
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65 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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66 </param>
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67 </repeat>
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68 <param name="ref_file" type="select" label="Using reference genome" >
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69 <options from_data_table="sam_fa_indexes">
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70 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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71 </options>
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72 <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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73 </param>
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74 </when>
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75 <when value="history"> <!-- FIX ME!!!! -->
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76 <repeat name="input_bams" title="BAM file" min="1" >
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77 <param name="input_bam" type="data" format="bam" label="BAM file" >
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78 </param>
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79 </repeat>
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80 <param name="ref_file" type="data" format="fasta" label="Using reference file" optional="True" />
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81 </when>
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82 </conditional>
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83
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84 <repeat name="regions" title="Restrict to regions" min="0" >
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85 <param name="chromosome" type="text" value="" optional="False" label="Chromosome" />
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86 <param name="start" type="integer" value="" optional="True" label="Start" />
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87 <param name="end" type="integer" value="" optional="True" label="End" />
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88 </repeat>
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89
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90 <!-- TODO: enhance filtering -->
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91 <param name="min_support_depth" type="integer" value="0" min="0" label="Minimum number of reads needed to consider a REF/ALT" />
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92 <param name="min_base_quality" type="integer" value="" label="Minimum base quality" optional="True" />
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93 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" />
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94
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95 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
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96 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with with possible alternate alleles"/>
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97
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98 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
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99
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100 <conditional name="advanced_options">
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101 <param name="advanced_options_selector" type="select" label="Show Advanced Options">
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102 <option value="basic" selected="True">Hide Advanced Options</option>
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103 <option value="advanced">Show Advanced Options</option>
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104 </param>
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105 <when value="basic">
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106 <!-- Do nothing here -->
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107 </when>
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108 <when value="advanced">
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109 <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM">
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110 <option value="uint8">uint8</option>
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111 <option value="uint16">uint16</option>
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112 <option value="uint32">uint32</option>
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113 <option value="uint64" selected="True">uint64</option>
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114 </param>
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115 <param name="safe" type="boolean" truevalue="--safe" falsevalue="" checked="False" label="Be extra safe"/>
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116 </when>
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117 </conditional>
1
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118
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119 </inputs>
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120 <outputs>
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121 <data format="vcf" name="output_vcf" />
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122 </outputs>
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123 <help>
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124 **What it does**
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125
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126 This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples.
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127
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128 User configurable options allow filtering reads that do not pass mapping or base quality thresholds and minimum per base read depth; user's can also specify the ploidy and whether to consider each strand separately.
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129
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130 In addition to calling alternate alleles based upon simple ratios of nucleotides at a position, per base nucleotide counts are also provided. A custom tag, NC, is used within the Genotype fields. The NC field is a comma-separated listing of nucleotide counts in the form of &lt;nucleotide&gt;=&lt;count&gt;, where a plus or minus character is prepended to indicate strand, if the strandedness option was specified.
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131
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132
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133 ------
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134
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135 **Inputs**
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136
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137 Accepts one or more BAM input files and a reference genome from the built-in list or from a FASTA file in your history.
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138
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139
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140 **Outputs**
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141
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142 The output is in VCF format.
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143
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144 Example VCF output line, without reporting by strand:
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145 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
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146
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147 Example VCF output line, when reporting by strand:
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148 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
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149
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150 **Options**
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151
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152 Reference Genome:
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153
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154 Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
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155
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156 Restrict to regions:
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157
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158 You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions.
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159
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160 Minimum number of reads needed to consider a REF/ALT:
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161
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162 This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
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163
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164 Minimum base quality:
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165
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166 The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
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167
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168 Minimum mapping quality:
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169
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170 The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
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171
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172 Ploidy:
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173
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174 The number of genotype calls to make at each reported position.
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175
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176 Only write out positions with with possible alternate alleles:
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177
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178 When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
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179
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180 Report counts by strand:
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181
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182 When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: &lt;strand&gt;&lt;BASE&gt;=&lt;COUNT&gt;.
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183
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184 Choose the dtype to use for storing coverage information:
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185
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186 This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
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187
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188 +--------+----------------------------+
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189 | name | maximum coverage value |
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190 +========+============================+
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191 | uint8 | 255 |
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192 +--------+----------------------------+
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193 | uint16 | 65,535 |
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194 +--------+----------------------------+
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195 | uint32 | 4,294,967,295 |
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196 +--------+----------------------------+
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197 | uint64 | 18,446,744,073,709,551,615 |
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198 +--------+----------------------------+
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199
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200 ------
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201
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202 **Citation**
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203
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204 If you use this tool, please cite Blankenberg D, et al. *In preparation.*
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205
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206 </help>
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207 <tests>
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208 <test>
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209 <param name="reference_source_selector" value="history" />
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210 <param name="input_bam" value="fake_phiX174_reads_1.bam" ftype="bam" />
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211 <param name="ref_file" value="phiX174.fasta" ftype="fasta" />
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212 <param name="regions" value="0" />
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213 <param name="min_support_depth" value="0" />
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214 <param name="min_base_quality" value="" />
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215 <param name="min_mapping_quality" value="" />
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216 <param name="ploidy" value="2" />
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217 <param name="variants_only" value="False" />
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218 <param name="use_strand" value="False" />
5
8398666758e3 Update options.
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219 <param name="advanced_options_selector" value="advanced" />
1
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220 <param name="coverage_dtype" value="uint8" />
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221 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
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222 </test>
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223 </tests>
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224
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225 </tool>