Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/calldiff_v17.xml @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
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1
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1 <tool id="cg_calldiff" name="CallDiff" version="1.7.1">
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2
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3 <description>Compares two Complete Genomics variant files.</description>
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4
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5 <requirements>
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6 <requirement type="package" version="1">cgatools17</requirement>
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7 </requirements>
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8
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9 <command> <!--run executable-->
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10 cgatools | head -1;
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11 cgatools calldiff
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12 --beta
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13 --reference ${crr.fields.crr_path}
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14 --variantsA $inputA
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15 --variantsB $inputB
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16 $validation
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17 $diploid
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18 --locus-stats-column-count $column
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19 --max-hypothesis-count $hypothesis
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20 --output-prefix cg_
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21 --reports `echo ${report1} ${report2} ${report3} ${report4} ${report5} | sed 's/ */,/g'`
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22 </command>
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23
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24 <inputs>
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25 <!--form field to select crr file-->
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26 <param name="crr" type="select" label="Reference Build">
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27 <options from_data_table="cg_anno_files" />
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28 </param>
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29
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30 <!-- input files -->
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31 <param name="inputA" type="data" format="cg_var,tabular" label="Var file A"></param>
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32 <param name="inputB" type="data" format="cg_var,tabular" label="Var file B"></param>
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33
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34 <!-- reports -->
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35 <param name="report1" type="select" label="Create report SuperlocusOutput">
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36 <option value="">no</option>
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37 <option value="SuperlocusOutput">yes</option>
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38 </param>
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39 <param name="report2" type="select" label="Create report SuperlocusStats">
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40 <option value="">no</option>
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41 <option value="SuperlocusStats">yes</option>
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42 </param>
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43 <param name="report3" type="select" label="Create report LocusOutput">
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44 <option value="">no</option>
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45 <option value="LocusOutput">yes</option>
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46 </param>
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47 <param name="report4" type="select" label="Create report LocusStats">
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48 <option value="">no</option>
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49 <option value="LocusStats">yes</option>
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50 </param>
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51 <param name="report5" type="select" label="Create report VariantOutput" help="Both variant files annotated by comparison results.If the somatic output report is requested, file A is also annotated with the same score ranks as produced in that report.">
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52 <option value="VariantOutput">yes</option>
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53 <option value="">no</option>
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54 </param>
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55
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56 <!-- parameters -->
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57 <param name="diploid" type="select" label="Use diploid variant model" help="Uses varScoreEAF instead of varScoreVAF in somatic score computations. Also, uses diploid variant model instead of variable allele mixture model.">
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58 <option value="">no</option>
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59 <option value="--diploid">yes</option>
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60 </param>
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61
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62 <param name="column" type="integer" label="Number of columns for locus compare classification in the locus stats file (default 15)" value="15"/>
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63
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64 <param name="hypothesis" type="integer" label="Maximum number of possible phasings to consider for a superlocus (default 32)" value="32"/>
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65
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66 <param name="validation" type="select" label="Reference cover validation" help="Turns on/off validation that all bases of a chromosome are covered by calls of the variant file.">
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67 <option value="">on</option>
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68 <option value="--no-reference-cover-validation">off</option>
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69 </param>
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70
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71 <!-- prefix for output file so you dont have to manually rename history items -->
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72 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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73 </inputs>
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74
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75 <outputs>
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76 <data format="tabular" name="output1" from_work_dir="cg_SuperlocusOutput.tsv" label="$fname ${tool.name} on ${on_string}: SuperlocusOutput">
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77 <filter>(report1 == 'SuperlocusOutput')</filter>
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78 </data>
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79 <data format="tabular" name="output2" from_work_dir="cg_SuperlocusStats.tsv" label="$fname ${tool.name} on ${on_string}: SuperlocusStats">
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80 <filter>(report2 == 'SuperlocusStats')</filter>
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81 </data>
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82 <data format="tabular" name="output3" from_work_dir="cg_LocusOutput.tsv" label="$fname ${tool.name} on ${on_string}: LocusOutput">
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83 <filter>(report3 == 'LocusOutput')</filter>
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84 </data>
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85 <data format="tabular" name="output4" from_work_dir="cg_LocusStats.tsv" label="$fname ${tool.name} on ${on_string}: LocusStats">
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86 <filter>(report4 == 'LocusStats')</filter>
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87 </data>
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88 <data format="tabular" name="output5a" from_work_dir="cg_VariantsA.tsv" label="$fname ${tool.name} on ${on_string}: VariantsA">
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89 <filter>(report5 == 'VariantOutput')</filter>
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90 </data>
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91 <data format="tabular" name="output5b" from_work_dir="cg_VariantsB.tsv" label="$fname ${tool.name} on ${on_string}: VariantsB">
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92 <filter>(report5 == 'VariantOutput')</filter>
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93 </data>
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94 </outputs>
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95
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96 <tests>
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97 <test>
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98 <param name="inputA" value="HCC1187_T_chr22.tsv" />
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99 <param name="inputA" value="HCC1187_N_chr22.tsv" />
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100 <param name="crr" value="hg18" />
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101 <param name="report1" value="SuperlocusOutput" />
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102 <param name="report2" value="" />
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103 <param name="report3" value="" />
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104 <param name="report4" value="" />
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105 <param name="report5" value="" />
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106 <param name="diploid" value="" />
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107 <param name="column" value="15" />
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108 <param name="hypothesis" value="" />
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109 <output name="output1" file="HCC1187_chr22_SuperLocusOutput.tsv" />
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110 </test>
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111 </tests>
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112
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113 <help>
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114 **What it does**
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115
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116 This tool compares two Complete Genomics variant files.
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117
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118 **cgatools 1.7.1 Documentation**
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119
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120 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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121
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122 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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123
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124 **Command line reference**::
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125
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126 COMMAND NAME
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127 calldiff - Compares two Complete Genomics variant files.
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128
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129 DESCRIPTION
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130 Compares two Complete Genomics variant files. Divides the genome up into
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131 superloci of nearby variants, then compares the superloci. Also refines the
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132 comparison to determine per-call or per-locus comparison results.
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133
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134 Comparison results are usually described by a semi-colon separated string,
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135 one per allele. Each allele's comparison result is one of the following
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136 classifications:
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137
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138 ref-identical The alleles of the two variant files are identical, and
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139 they are consistent with the reference.
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140 alt-identical The alleles of the two variant files are identical, and
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141 they are inconsistent with the reference.
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142 ref-consistent The alleles of the two variant files are consistent,
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143 and they are consistent with the reference.
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144 alt-consistent The alleles of the two variant files are consistent,
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145 and they are inconsistent with the reference.
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146 onlyA The alleles of the two variant files are inconsistent,
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147 and only file A is inconsistent with the reference.
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148 onlyB The alleles of the two variant files are inconsistent,
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149 and only file B is inconsistent with the reference.
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150 mismatch The alleles of the two variant files are inconsistent,
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151 and they are both inconsistent with the reference.
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152 phase-mismatch The two variant files would be consistent if the
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153 hapLink field had been empty, but they are
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154 inconsistent.
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155 ploidy-mismatch The superlocus did not have uniform ploidy.
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156
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157 In some contexts, this classification is rolled up into a simplified
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158 classification, which is one of "identical", "consistent", "onlyA",
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159 "onlyB", or "mismatch".
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160
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161 A good place to start looking at the results is the superlocus-output file.
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162 It has columns defined as follows:
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163
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164 SuperlocusId An identifier given to the superlocus.
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165 Chromosome The name of the chromosome.
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166 Begin The 0-based offset of the start of the superlocus.
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167 End The 0-based offset of the base one past the end of the
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168 superlocus.
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169 Classification The match classification of the superlocus.
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170 Reference The reference sequence.
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171 AllelesA A semicolon-separated list of the alleles (one per
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172 haplotype) for variant file A, for the phasing with the
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173 best comparison result.
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174 AllelesB A semicolon-separated list of the alleles (one per
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175 haplotype) for variant file B, for the phasing with the
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176 best comparison result.
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177
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178 The locus-output file contains, for each locus in file A and file B that is
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179 not consistent with the reference, an annotated set of calls for the locus.
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180 The calls are annotated with the following columns:
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181
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182 SuperlocusId The id of the superlocus containing the locus.
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183 File The variant file (A or B).
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184 LocusClassification The locus classification is determined by the
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185 varType column of the call that is inconsistent
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186 with the reference, concatenated with a
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187 modifier that describes whether the locus is
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188 heterozygous, homozygous, or contains no-calls.
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189 If there is no one variant in the locus (i.e.,
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190 it is heterozygous alt-alt), the locus
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191 classification begins with "other".
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192 LocusDiffClassification The match classification for the locus. This is
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193 defined to be the best of the comparison of the
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194 locus to the same region in the other file, or
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195 the comparison of the superlocus.
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196
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197 The somatic output file contains a list of putative somatic variations of
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198 genome A. The output includes only those loci that can be classified as
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199 snp, del, ins or sub in file A, and are called reference in the file B.
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200 Every locus is annotated with the following columns:
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201
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202 VarCvgA The totalReadCount from file A for this locus
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203 (computed on the fly if file A is not a
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204 masterVar file).
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205 VarScoreA The varScoreVAF from file A, or varScoreEAF if
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206 the "--diploid" option is used.
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207 RefCvgB The maximum of the uniqueSequenceCoverage
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208 values for the locus in genome B.
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209 RefScoreB Minimum of the reference scores of the locus in
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210 genome B.
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211 SomaticCategory The category used for determining the
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212 calibrated scores and the SomaticRank.
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213 VarScoreACalib The calibrated variant score of file A, under
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214 the model selected by using or not using the
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215 "--diploid" option, and corrected for the count
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216 of heterozygous variants observed in this
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217 genome. See user guide for more information.
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218 VarScoreBCalib The calibrated reference score of file B, under
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219 the model selected by using or not using the
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220 "--diploid" option, and corrected for the count
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221 of heterozygous variants observed in this
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222 genome. See user guide for more information.
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223 SomaticRank The estimated rank of this somatic mutation,
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224 amongst all true somatic mutations within this
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225 SomaticCategory. The value is a number between
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226 0 and 1; a value of 0.012 means, for example,
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227 that an estimated 1.2% of the true somatic
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228 mutations in this somaticCategory have a
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229 somaticScore less than the somaticScore for
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230 this mutation. See user guide for more
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231 information.
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232 SomaticScore An integer that provides a total order on
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233 quality for all somatic mutations. It is equal
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234 to -10*log10( P(false)/P(true) ), under the
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235 assumption that this genome has a rate of
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236 somatic mutation equal to 1/Mb for
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237 SomaticCategory snp, 1/10Mb for SomaticCategory
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238 ins, 1/10Mb for SomaticCategory del, and 1/20Mb
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239 for SomaticCategory sub. The computation is
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240 based on the assumptions described in the user
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241 guide, and is affected by choice of variant
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242 model selected by using or not using the
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243 "--diploid" option.
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244 SomaticQuality Equal to VQHIGH for all somatic mutations where
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245 SomaticScore &gt;= -10. Otherwise, this column is
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246 empty.
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247
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248 OPTIONS
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249 -h [ --help ]
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250 Print this help message.
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251
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252 --reference arg
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253 The input crr file.
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254
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255 --variantsA arg
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256 The "A" input variant file.
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257
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258 --variantsB arg
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259 The "B" input variant file.
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260
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261 --output-prefix arg
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262 The path prefix for all output reports.
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263
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264 --reports arg (=SuperlocusOutput,SuperlocusStats,LocusOutput,LocusStats)
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265 Comma-separated list of reports to generate. (Beware any reports whose
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266 name begins with "Debug".) A report is one of:
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267 SuperlocusOutput Report for superlocus classification.
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268 SuperlocusStats Report for superlocus classification stats.
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269 LocusOutput Report for locus classification.
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270 LocusStats Report for locus stats.
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271 VariantOutput Both variant files annotated by comparison
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272 results.If the somatic output report is
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273 requested, file A is also annotated with the
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274 same score ranks as produced in that report.
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275 SomaticOutput Report for the list of simple variations that
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276 are present only in file "A", annotated with
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277 the score that indicates the probability of
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278 the variation being truly somatic. Requires
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279 beta, genome-rootA, and genome-rootB options
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280 to be provided as well. Note: generating this
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281 report slows calldiff by 10x-20x.
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282 DebugCallOutput Report for call classification.
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283 DebugSuperlocusOutput Report for debug superlocus information.
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284 DebugSomaticOutput Report for distribution estimates used for
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285 somatic rescoring. Only produced if
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286 SomaticOutput is also turned on.
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287
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288 --diploid
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289 Uses varScoreEAF instead of varScoreVAF in somatic score computations.
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290 Also, uses diploid variant model instead of variable allele mixture
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291 model.
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292
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293 --locus-stats-column-count arg (=15)
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294 The number of columns for locus compare classification in the locus
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295 stats file.
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296
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297 --max-hypothesis-count arg (=32)
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298 The maximum number of possible phasings to consider for a superlocus.
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299
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300 --no-reference-cover-validation
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301 Turns off validation that all bases of a chromosome are covered by
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302 calls of the variant file.
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303
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304 --genome-rootA arg
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305 The "A" genome directory, for example /data/GS00118-DNA_A01; this
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306 directory is expected to contain ASM/REF and ASM/EVIDENCE
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307 subdirectories.
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308
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309 --genome-rootB arg
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310 The "B" genome directory.
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311
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312 --calibration-root arg
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313 The directory containing calibration data. For example, there should
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314 exist a file calibration-root/0.0.0/metrics.tsv.
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315
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316 --beta
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317 This flag enables the SomaticOutput report, which is beta
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318 functionality.
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319
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320 SUPPORTED FORMAT_VERSION
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321 0.3 or later
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322 </help>
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323 </tool>