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