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1 <tool id="somatic_sniper_tool" name="Somatic Sniper" version="1.0.2">
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2 <description>: identify single nucleotide positions that are different between tumor and normal</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.6">samtools</requirement>
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5 <requirement type="package" version="unstable">somatic-sniper</requirement>
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6 </requirements>
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7 <command interpreter="perl">
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8 somatic_sniper_wrapper.pl
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9
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10 "NORMAL::$normal"
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11 "TUMOR::$tumor"
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12 "OUTPUT::$snp_output"
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13 "OPTION::-F $output"
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14
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15 #if $option.option == "modify_parameters":
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16 "OPTION::-q $option.readFilter"
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17 "OPTION::-Q $option.somaticFilter"
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18 "OPTION::-s $option.mutationPrior"
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19 #if str($option.disablePriors) == "true"
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20 "OPTION::-p"
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21 #end if
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22 #end if
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23
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24 "OPTION::-f $reference.fields.path"
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25
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26
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27 </command>
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28 <inputs>
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29 <param name="reference" type="select" label="Select a reference genome">
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30 <options from_data_table="all_fasta">
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31 <filter type="sort_by" column="2" />
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32 <validator type="no_options" message="No indexes are available" />
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33 </options>
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34 </param>
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35
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36 <param format="bam" name="normal" type="data" label="Normal sample" help=""/>
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37 <param format="bam" name="tumor" type="data" label="Tumor Sample" help=""/>
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38 <param name="output" type="select" label="Output Type" help="" optional="true">
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39 <option value="classic" selected="true">Classic</option>
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40 <option value="vcf">VCF</option>
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41 <option value="bed">BED</option>
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42 </param>
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43
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44
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45 <conditional name="option">
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46 <param name="option" type="select" label="Optional Parameters" help="" optional="true">
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47 <option value="default_parameters" selected="true">Default Parameters</option>
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48 <option value="modify_parameters">Modify Parameters</option>
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49 </param>
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50 <when value="modify_parameters">
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51
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52 <param name="readFilter" label="filtering reads with mapping quality less than" type="integer" value="0" optional="true" />
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53 <param name="somaticFilter" label="filtering somatic snv output with somatic quality less than" type="integer" value="15" optional="true" />
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54 <param name="disablePriors" type="select" label="disable priors in the somatic calculation. Increases sensitivity for solid tumors" help="" optional="true">
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55 <option value="true" >true</option>
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56 <option value="false" selected="true">false</option>
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57 </param>
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58 <param name="mutationPrior" label="prior probability of a somatic mutation" type="float" value="0.10000" optional="true" />
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59
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60 </when>
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61
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62 </conditional>
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63
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64 </inputs>
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65 <outputs>
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66 <data name="snp_output" format="text" label="${tool.name} result on ${on_string}" />
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67 </outputs>
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68 <help>
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69 |
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70
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71
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72 **Reference**
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73
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74 http://gmt.genome.wustl.edu/somatic-sniper/current/
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75
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76 -----
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77
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78 **What it does**
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79
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80 The purpose of this program is to identify single nucleotide positions that are different between tumor and normal
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81 (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the
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82 differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood
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83 model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are
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84 different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255)
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85 that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and
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86 255 means there is a probability of 1 – 10(255/-10) that the genotypes are different between tumor and normal. This is consistent
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87 with how the SAM format reports such probabilities.
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88
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89 bam-somaticsniper [options] -f ref.fasta tumor.bam normal.bam snp_output_file
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90
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91 Bam files must contain LB tag in @RG line.
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92 Picard tools can be used to add lines to BAM headers.
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93
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94 -----
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95
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96 **Required Parameters**
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97
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98 ::
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99
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100 -f FILE REQUIRED reference sequence in the FASTA format
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101
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102 -----
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103
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104 **Options**
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105
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106 ::
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107
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108 -q INT filtering reads with mapping quality less than INT [0]
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109
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110 -Q INT filtering somatic snv output with somatic quality less than INT [15]
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111
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112 -p FLAG disable priors in the somatic calculation. Increases sensitivity for solid tumors
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113
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114 -J FLAG Use prior probabilities accounting for the somatic mutation rate
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115
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116 -s FLOAT prior probability of a somatic mutation (implies -J) [0.010000]
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117
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118 -T FLOAT theta in maq consensus calling model (for -c/-g) [0.850000]
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119
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120 -N INT number of haplotypes in the sample (for -c/-g) [2]
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121
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122 -r FLOAT prior of a difference between two haplotypes (for -c/-g) [0.001000]
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123
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124 -F STRING select output format [classic]
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125 Available formats:
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126 classic
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127 vcf
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128 bed
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129
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130 -----
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131
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132 **File Formats**
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133
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134 ::
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135
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136 Classic:
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137
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138 Each line contains the following tab-separated values:
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139
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140 1. Chromosome
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141 2. Position
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142 3. Reference base
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143 4. IUB genotype of tumor
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144 5. IUB genotype of normal
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145 6. Somatic Score
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146 7. Tumor Consensus quality
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147 8. Tumor variant allele quality
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148 9. Tumor mean mapping quality
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149 10. Normal Consensus quality
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150 11. Normal variant allele quality
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151 12. Normal mean mapping quality
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152 13. Depth in tumor (# of reads crossing the position)
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153 14. Depth in normal (# of reads crossing the position)
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154 15. Mean base quality of reads supporting reference in tumor
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155 16. Mean mapping quality of reads supporting reference in tumor
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156 17. Depth of reads supporting reference in tumor
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157 18. Mean base quality of reads supporting variant(s) in tumor
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158 19. Mean mapping quality of reads supporting variant(s) in tumor
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159 20. Depth of reads supporting variant(s) in tumor
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160 21. Mean base quality of reads supporting reference in normal
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161 22. Mean mapping quality of reads supporting reference in normal
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162 23. Depth of reads supporting reference in normal
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163 24. Mean base quality of reads supporting variant(s) in normal
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164 25. Mean mapping quality of reads supporting variant(s) in normal
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165 26. Depth of reads supporting variant(s) in normal
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166
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167
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168
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169 </help>
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170 </tool>
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171
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172
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