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annotate sniffles.xml @ 3:09f5c6f3088a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
author iuc
date Thu, 26 Sep 2024 11:44:13 +0000
parents 3f6f028f418f
children 43fffeed243f
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1 <tool id="sniffles" name="sniffles" version="@TOOL_VERSION@+galaxy0" profile="23.0">
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2 <description>Structural variation caller using third generation sequencing</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.4</token>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">sniffles</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">sniffles</requirement>
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11 </requirements>
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12 <version_command>
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13 <![CDATA[ sniffles --version ]]>
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14 </version_command>
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15 <command detect_errors="exit_code">
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16 <![CDATA[
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17 ln -f -s '${input}' input.bam &&
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18 ln -f -s '${input.metadata.bam_index}' input.bam.bai &&
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19 #if $reference_genome.genome_type_select != "None":
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20 #if $reference_genome.genome_type_select == "indexed":
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21 ln -f -s '${reference_genome.genome.fields.path}' 'reference.fa' &&
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22 #else:
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23 ln -f -s '${reference_genome.genome}' 'reference.fa' &&
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24 #end if
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25 #end if
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26 sniffles
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27 -t \${GALAXY_SLOTS:-2}
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28 -i 'input.bam'
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29 -v '$output'
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30 ## must set allow-overwrite since the new output vcf file exists
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31 --allow-overwrite
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32 #if $reference_genome.genome_type_select != "None":
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33 --reference 'reference.fa'
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34 #end if
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35 ## general_options
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36 --minsupport '$general_options.minsupport'
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37 --max-splits-kb '$general_options.maxsplitskb'
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38 --minsvlen '$general_options.minsvlen'
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39 --mapq '$general_options.mapq'
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40 --min-alignment-length '$general_options.minalignmentlength'
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41 ## clustering_options
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42 --cluster-binsize '$clustering_options.clusterbinsize'
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43 --cluster-r '$clustering_options.clusterr'
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44 ## advanced_options
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45 $advanced_options.mosaic
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46 ]]>
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47 </command>
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48 <inputs>
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49 <param type="data" name="input" format="bam" label="Input BAM file"/>
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50 <conditional name="reference_genome">
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51 <param name="genome_type_select" type="select" label="Reference genome source is required for deletion SV sequence reporting"
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52 help="Optional: Select None, a built-in or history reference genome fasta">
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53 <option value="None" selected="True">No reference fasta - do not report DEL SV sequence</option>
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54 <option value="indexed">Use a Galaxy server built-in genome</option>
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55 <option value="history">Use a genome fasta file from the current history</option>
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56 </param>
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57 <when value="None">
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58 <param name="genome" type="text" value="None"/>
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59 </when>
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60 <when value="indexed">
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61 <param name="genome" type="select" optional="false" label="Select a built in reference genome or custom genome"
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62 help="If not listed, add a custom genome or use a reference genome from the history">
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63 <options from_data_table="all_fasta">
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64 <validator message="No genomes are available " type="no_options"/>
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65 </options>
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66 </param>
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67 </when>
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68 <when value="history">
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69 <param name="genome" type="data" format="fasta" optional="false" label="Select the reference genome fasta from the current history"/>
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70 </when>
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71 </conditional>
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72 <section name="general_options" title="Set general options" expanded="False">
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73 <param argument="--minsupport" type="text" value="auto" label="Minimum Support" help="Minimum number of reads that support a SV. [auto]. Smaller support values -> more SV reported"/>
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74 <param name="maxsplitskb" type="float" value="0.1" min="0" label="Maximum Number of Splits per KB" help="Additional number of splits per kilobase read sequence allowed before reads are ignored [0.1]" />
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75 <param name="minsvlen" type="integer" value="50" min="2" label="Minimum Length" help="Minimum length of SV to be reported. [50]"/>
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76 <param name="mapq" type="integer" value="20" min="0" label="Minimum Mapping Quality" help="Minimum Mapping Quality to consider. [20]"/>
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77 <param name="minalignmentlength" type="integer" value="100" min="0" label="Minimum alignment length" help="Reads with alignments shorter than this length (in bp) will be ignored"/>
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78 </section>
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79 <section name="clustering_options" title="Clustering/phasing and genotyping options" expanded="False">
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80 <param argument="--clusterbinsize" value="100" type="integer" min="0" label="Cluster bin size" help="Initial screening bin size [100]"/>
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81 <param argument="--clusterr" type="float" value="2.5" min="0.0" label="Cluster Multiplier" help="Multiplier for SV start position standard deviation criterion in cluster merging [2.5]"/>
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82 </section>
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83 <section name="advanced_options" title="Advanced options" expanded="False">
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84 <param name="mosaic" type="boolean" value="False" truevalue="--mosaic" falsevalue="" label="Mosaic mode" help="Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)" />
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85 </section>
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86 </inputs>
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87 <outputs>
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88 <data name="output" format="vcf" label="${tool.name} on ${on_string}"/>
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89 </outputs>
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90 <tests>
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91 <test> <!-- test 1 - standard run -->
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92 <param name="input" value="reads_region.bam"/>
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93 <output name="output" file="expected_output.vcf" lines_diff="4"/>
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94 </test>
1
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95 <test> <!-- test 2 - filter on mapq -->
0
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96 <param name="input" value="reads_region.bam"/>
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97 <param name="mapq" value="0"/>
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98 <output name="output" file="expected_output2.vcf" lines_diff="4"/>
0
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99 </test>
1
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100 <test> <!-- test 3 min support test -->
0
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101 <param name="input" value="reads_region.bam"/>
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102 <param name="minsupport" value="1"/>
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103 <output name="output" file="expected_outcome3.vcf" lines_diff="4"/>
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104 </test>
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105 <test> <!-- test 4 - clustering -->
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106 <param name="input" value="reads_region.bam"/>
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107 <param name="clusterbinsize" value="5"/>
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108 <output name="output" file="expected_outcome4.vcf" lines_diff="4"/>
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109 </test>
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110 <test> <!-- test 5 - Advanced - mosaic -->
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111 <param name="input" value="reads_region.bam"/>
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112 <param name="mosaic" value="--mosaic"/>
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113 <output name="output" file="expected_outcome5.vcf" lines_diff="4"/>
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114 </test>
3
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115 <test> <!-- test 6 - reference -->
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116 <param name="input" value="reads_region.bam"/>
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117 <conditional name="reference_genome">
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118 <param name="genome_type_select" value="history"/>
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119 <param name="genome" value="humsamp.fa"/>
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120 <param name="genome.ext" value="fasta"/>
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121 </conditional>
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122 <output name="output" file="expected_outcome6.vcf" lines_diff="4"/>
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123 </test>
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124 </tests>
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125 <help>
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126 <![CDATA[
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127 ########
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128 Sniffles
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129 ########
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130
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131 What is Sniffles?
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132 *****************
1
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133 Sniffles is a SV caller for long reads. Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.
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134
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135 SV are larger events on the genome (e.g. deletions, duplications, insertions, inversions and translocations).
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136 Sniffles can detect all of these type and more such as nested SVs (e.g. inversion flanked by deletions or an inverted duplication).
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137
1
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138 Inputs
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139 ******
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140
1
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141 Known to work with Minimap2 bam as input
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142
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143 Parameters
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144 **********
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145
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146 General
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147 -------
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148
1
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149
0
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150 +---------------------------+-----------------------------------------------------------------------+
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151 | Parameter | Description |
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152 +===========================+=======================================================================+
1
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153 | Minimum Support | Minimum number of reads supporting a SV to be reported. Default:auto |
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154 +---------------------------+-----------------------------------------------------------------------+
1
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155 | Maximum Number of Splits | Maximum number of split segments per kb a read is aligned at before |
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156 | | it is ignored. Default: 7 |
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157 +---------------------------+-----------------------------------------------------------------------+
1
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158 | Minimum SV Length | Minimum length of SV to be reported. Default: 50bp |
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159 +---------------------------+-----------------------------------------------------------------------+
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160 | Minimum Mapping Quality | Minimum mapping quality of alignment to be taken into account. |
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161 | | Default: 20 |
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162 +---------------------------+-----------------------------------------------------------------------+
1
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163 | Minimum alignment length | Reads with less length aligned will be ignored. Default 100 |
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164 +---------------------------+-----------------------------------------------------------------------+
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165
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166
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167 Clustering Options
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168 ------------------
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169
1
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170
0
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171 +----------------------------------------+-----------------------------------------------------------------------+
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172 | Parameter | Description |
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173 +========================================+=======================================================================+
1
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174 | Cluster bin size | Initial cluster bin size. Default 100 |
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175 +----------------------------------------+-----------------------------------------------------------------------+
1
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176 | Cluster Multiplier | Multiplier for SV start position standard deviation criterion in |
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177 | | cluster merging [2.5] |
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178 +----------------------------------------+-----------------------------------------------------------------------+
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179
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180
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181 Advanced Options
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182 ----------------
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183
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184
1
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185 +----------------------------------------+------------------------------------------------------------------------------+
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186 | Parameter | Description |
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187 +========================================+==============================================================================+
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188 | Mosaic | Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)|
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189 +----------------------------------------+------------------------------------------------------------------------------+
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190
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191
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192 Output
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193 ******
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194
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195 VCF Info field description
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196
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197 Sniffles report multiple information in the Info field. The entries are delimited by:
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198
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199 +-------------------+------------------------------------------------------------------------------------------------------+
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200 | IMPRECISE/PRECISE | Indicates the confidence of the exact breakpoint positions (bp). |
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201 +-------------------+------------------------------------------------------------------------------------------------------+
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202 | CHR2= | The chromosome of the second breakpoint of the SV reported. |
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203 +-------------------+------------------------------------------------------------------------------------------------------+
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204 | END= | The position (bp) of the second breakpoint of the SV reported. |
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205 +-------------------+------------------------------------------------------------------------------------------------------+
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206 | ZMW= | For PacBio based reads, shows the number of ZMW that support the SV. |
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207 +-------------------+------------------------------------------------------------------------------------------------------+
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208 | SVTYPE= | The type of the SV. (see Alt field above) |
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209 +-------------------+------------------------------------------------------------------------------------------------------+
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210 | SUPTYPE= | Indicates what evidence supports the SVs (SR: Split Reads, AL: Alignment, NR: Noisy Region). |
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211 +-------------------+------------------------------------------------------------------------------------------------------+
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212 | STD_quant_start= | The standard deviation of the start breakpoints. |
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213 +-------------------+------------------------------------------------------------------------------------------------------+
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214 | STD_quant_stop= | The standard deviation of the stop breakpoints. |
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215 +-------------------+------------------------------------------------------------------------------------------------------+
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216 | RNAMES= | A comma separated list of read names that support the SV event. Controlled by -n Parameter. |
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217 +-------------------+------------------------------------------------------------------------------------------------------+
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218 | SVLEN= | Indicates the length of SVs. |
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219 +-------------------+------------------------------------------------------------------------------------------------------+
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220 | STRANDS= | Strand information at both breakpoints. |
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221 +-------------------+------------------------------------------------------------------------------------------------------+
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222 | SEQ= | If reportable shows the sequence of the indels. |
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223 +-------------------+------------------------------------------------------------------------------------------------------+
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224 | RE= | Number of reads supporting the variance. |
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225 +-------------------+------------------------------------------------------------------------------------------------------+
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226 | AF= | Allele frequency (only if run with –genotype) |
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227 +-------------------+------------------------------------------------------------------------------------------------------+
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228
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229 Source: https://github.com/fritzsedlazeck/Sniffles
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230 ]]>
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231 </help>
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232 <citations>
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233 <citation type="doi">10.1038/s41587-023-02024-y</citation>
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234 </citations>
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235 </tool>