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1 <tool id="breakdancer" name="breakdancer" version="1.4.4">
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2 <requirements>
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3 <requirement type="package" version="1.4.4">breakdancer</requirement>
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4 </requirements>
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5
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6 <description>detection of structural variants</description>
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7
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8 <parallelism method="basic"></parallelism>
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9
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10 <command interpreter="python">
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11 breakdancer.py
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12 <!-- required -->
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13 -i1 $inputBamFile
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14 -o1 $outputRawFile
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15 <!-- optional -->
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16 -o2 $outputVcfFile
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17 -o $chromosome
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18 -s $minLength
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19 -c $cutoff
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20 -m $maxSvSize
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21 -q $minMapQuality
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22 -r $minReadDepth
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23 -x $maxHaploidCov
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24 -b $bufferSize
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25 #if $onlyTrans:
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26 -t
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27 #end if
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28 -d $prefix
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29 #if $bedFormat:
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30 -g
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31 #end if
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32 <!-- -l
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33 -a
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34 -h
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35 -y -->
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36 <!-- parser.add_argument('-l', dest='matePair', required=False, help='analyze Illumina long insert (mate-pair) library')
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37 # parser.add_argument('-a', dest='sortByLibrary', action='store_true', help='print out copy number and support reads per library rather than per bam', default=False)
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38 # parser.add_argument('-h', dest='', action='store_true', help='print out Allele Frequency column', default=False)
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39 parser.add_argument('-y', dest='scoreFilter', type=int, required=False, help='output score filter', default=30) -->
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40
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41 </command>
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42
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43 <inputs>
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44 <param name="inputBamFile" format="bam" type="data" label="input bam file" />
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45 <!-- optional -->
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46 <param name="chromosome" type="text" label="operate on a single chromosome" value="" />
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47 <param name="minLength" type="integer" label="minimum length of a region" value="7" />
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48 <param name="cutoff" type="integer" label="cutoff in unit of standard deviation" value="3" />
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49 <param name="maxSvSize" type="integer" label="maximum SV size" value="1000000000" />
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50 <param name="minMapQuality" type="integer" label="minimum alternative mapping quality" value="35" />
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51 <param name="minReadDepth" type="integer" label="minimum number of read pairs required to establish a connection" value="2" />
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52 <param name="maxHaploidCov" type="integer" label="maximum threshold of haploid sequence coverage for regions to be ignored" value="1000" />
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53 <param name="bufferSize" type="integer" label="buffer size for building connection" value="100" />
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54 <param name="onlyTrans" type="boolean" label="only detect transchromosomal rearrangement" checked="False" />
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55 <param name="bufferSize" type="text" label="prefix of fastq files that SV supporting reads will be saved by library" value="" />
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56 <param name="bedFormat" type="boolean" label="dump SVs and supporting reads in BED format for GBrowse" checked="False" />
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57 </inputs>
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58
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59 <outputs>
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60 <data name="outputRawFile" format="tabular" />
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61 <data name="outputVcfFile" format="vcf" />
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62 </outputs>
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63
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64 <help>
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65 BreakDancer, released under GPLv3, is a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs.
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66 BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.
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67 BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs.
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68 Please read our paper for detailed algorithmic description. http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html
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69
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70 The input is a set of map files produced by a front-end aligner such as MAQ, BWA, NovoAlign and Bfast
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71
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72 The output format
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73 ----------------------
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74 BreakDancer's output file consists of the following columns:
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75
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76 1. Chromosome 1
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77 2. Position 1
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78 3. Orientation 1
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79 4. Chromosome 2
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80 5. Position 2
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81 6. Orientation 2
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82 7. Type of a SV
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83 8. Size of a SV
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84 9. Confidence Score
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85 10. Total number of supporting read pairs
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86 11. Total number of supporting read pairs from each map file
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87 12. Estimated allele frequency
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88 13. Software version
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89 14. The run parameters
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90 </help>
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91 </tool> |
