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annotate lumpy.xml @ 1:a006d42dd759 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
author drosofff
date Tue, 06 Dec 2016 09:29:31 -0500
parents 8b3daa745d9b
children b1e152172de9
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8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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1 <tool id="lumpy" name="lumpy-sv" version="0.1">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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2 <description>find structural variants</description>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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3 <requirements>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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4 <requirement type="package" version="0.2.12">lumpy-sv</requirement>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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5 <requirement type="package" version="1.3.1">samtools</requirement>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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6 <requirement type="package" version="1.11.2">numpy</requirement>
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7 </requirements>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Tool exception" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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10 </stdio>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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11 <version_command>lumpy --version</version_command>
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12 <command><![CDATA[
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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13 ln -f -s "$input_file" input.bam &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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14 #if $seq_method.seq_method_list == "paired-end":
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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15 samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" &&
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16 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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17 samtools sort input.discordants.unsorted.bam > input.discordants.bam &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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18 samtools sort input.splitters.unsorted.bam > input.splitters.bam &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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19 samtools view -r readgroup input.bam
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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20 |tail -n +$seq_method.additional_params.samplingValue
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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21 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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22 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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23 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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24 lumpy -mw 4 -tt 0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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25 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$seq_method.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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26 -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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27 mv input.discordants.bam $discordants &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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28 mv input.splitters.bam $splits &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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29 mv input.lib.histo $histogram &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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30 mv output.vcf $vcf_call &&
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31 rm input.discordants.unsorted.bam input.splitters.unsorted.bam meandev.txt
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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32 #end if
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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33 #if $seq_method.seq_method_list == "single-read":
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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34 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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35 lumpy -mw 4 -tt 0
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36 -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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37 mv input.splitters.unsorted.bam $splits &&
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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38 mv output.vcf $vcf_call
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39 #end if
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40
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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41 ]]></command>
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42 <!-- basic error handling -->
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43 <inputs>
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44 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
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45 <conditional name="seq_method">
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46 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
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47 <option selected="True" value="paired-end">Paired-end sequencing</option>
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48 <option value="single-read">Single-read sequencing</option>
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49 </param>
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50 <when value="paired-end">
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51 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
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52 <section name="additional_params" title="Additional Options" expanded="False">
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53 <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" />
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54 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" />
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55 <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" />
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56 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
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57 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
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58 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
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59 </section>
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60 </when>
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61 <when value="single-read">
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62 <section name="additional_params" title="Additional Options" expanded="False">
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63 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
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64 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
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65 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
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66 </section>
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67 </when>
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68
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69 </conditional>
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70
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71 </inputs>
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72
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73 <outputs>
1
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74 <data format="tabular" name="histogram" type="data" label="Lumpy on ${input_file.element_identifier}: Fragment size distribution">
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75 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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76 </data>
1
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77 <data format="bam" name="splits" type="data" label="Lumpy on ${input_file.element_identifier}: Split Reads (Bam format)"/>
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78 <data format="bam" name="discordants" type="data" label="Lumpy on ${input_file.element_identifier}: Discordant Pairs (Bam format)">
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79 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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80 </data>
1
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81 <data format="vcf" name="vcf_call" type="data" label="Lumpy on ${input_file.element_identifier}: Variant Calling (vcf format)"/>
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82 </outputs>
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83
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84 <tests>
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85 <test>
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86 <param name="input_file" value="sr.input.bam" ftype="bam"/>
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87 <param name="seq_method_list" value="single-read" />
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88 <param name="back_distance" value="10"/>
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89 <param name="weight" value="1" />
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90 <param name="min_mapping_threshold" value="20" />
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91 <output name="vcf_call" file="output.vcf" ftype="vcf"/>
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92 </test>
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93 </tests>
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94
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95 <help>
1
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96
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97 **lumpy-sv manual**
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98
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99 Read the lumpy-sv_ documentation for details on using lumpy.
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100
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101 .. _lumpy-sv: https://github.com/arq5x/lumpy-sv
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102
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103 **lumpy options**
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104
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105 v 0.2.13
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106 Author: Ryan Layer (rl6sf@virginia.edu)
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107
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108 Summary: Find structural variations in various signals.
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109
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110 Options::
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111
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112 -g Genome file (defines chromosome order)
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113 -e Show evidence for each call
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114 -w File read windows size (default 1000000)
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115 -mw minimum weight for a call
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116 -msw minimum per-sample weight for a call
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117 -tt trim threshold
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118 -x exclude file bed file
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119 -t temp file prefix, must be to a writeable directory
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120 -P output probability curve for each variant
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121 -b output BEDPE instead of VCF
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122 -sr bam_file:&lt;file name&gt;,
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123 id:&lt;sample name&gt;,
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124 back_distance:&lt;distance&gt;,
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125 min_mapping_threshold:&lt;mapping quality&gt;,
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126 weight:&lt;sample weight&gt;,
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127 min_clip:&lt;minimum clip length&gt;,
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128 read_group:&lt;string&gt;
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129
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130 -pe bam_file:&lt;file name&gt;,
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131 id:&lt;sample name&gt;,
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132 histo_file:&lt;file name&gt;,
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133 mean:&lt;value&gt;,
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134 stdev:&lt;value&gt;,
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135 read_length:&lt;length&gt;,
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136 min_non_overlap:&lt;length&gt;,
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137 discordant_z:&lt;z value&gt;,
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138 back_distance:&lt;distance&gt;,
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139 min_mapping_threshold:&lt;mapping quality&gt;,
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140 weight:&lt;sample weight&gt;,
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141 read_group:&lt;string&gt;
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142
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143 -bedpe bedpe_file:&lt;bedpe file&gt;,
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144 id:&lt;sample name&gt;,
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145 weight:&lt;sample weight&gt;
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146
0
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147 </help>
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148
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149 <citations>
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150 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
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151 </citations>
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152 </tool>