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comparison breakdancer.xml @ 11:a8f3dba37a92 draft

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author jeremie
date Wed, 02 Jul 2014 10:00:43 -0400
parents 44d381ebe8a5
children c220f4acef3f
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10:a6f66f70d166 11:a8f3dba37a92
1 <tool id="breakdancer" name="breakdancer" version="1.4.4"> 1 <tool id="breakdancer" name="breakdancer" version="1.4.4">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.4.4">breakdancer</requirement> 3 <requirement type="package" version="1.4.4">breakdancer</requirement>
4 </requirements> 4 </requirements>
5 5
6 <description> 6 <description>detection of structural variants</description>
7 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. 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. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs. Please read our paper for detailed algorithmic description. http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html
8
9 The input is a set of map files produced by a front-end aligner such as MAQ, BWA, NovoAlign and Bfast
10
11 The output format
12 ----------------------
13 BreakDancer's output file consists of the following columns:
14
15 1. Chromosome 1
16 2. Position 1
17 3. Orientation 1
18 4. Chromosome 2
19 5. Position 2
20 6. Orientation 2
21 7. Type of a SV
22 8. Size of a SV
23 9. Confidence Score
24 10. Total number of supporting read pairs
25 11. Total number of supporting read pairs from each map file
26 12. Estimated allele frequency
27 13. Software version
28 14. The run parameters
29 </description>
30 7
31 <parallelism method="basic"></parallelism> 8 <parallelism method="basic"></parallelism>
32 9
33 <command interpreter="python"> 10 <command interpreter="python">
34 breakdancer.py 11 breakdancer.py
65 42
66 <inputs> 43 <inputs>
67 <param name="inputBamFile" format="bam" type="data" label="input bam file" /> 44 <param name="inputBamFile" format="bam" type="data" label="input bam file" />
68 <!-- optional --> 45 <!-- optional -->
69 <param name="chromosome" type="text" label="operate on a single chromosome" value="" /> 46 <param name="chromosome" type="text" label="operate on a single chromosome" value="" />
70 <param name="chromosome" type="integer" label="minimum length of a region" value="7" /> 47 <param name="minLength" type="integer" label="minimum length of a region" value="7" />
71 <param name="cutoff" type="integer" label="cutoff in unit of standard deviation" value="3" /> 48 <param name="cutoff" type="integer" label="cutoff in unit of standard deviation" value="3" />
72 <param name="maxSvSize" type="integer" label="maximum SV size" value="1000000000" /> 49 <param name="maxSvSize" type="integer" label="maximum SV size" value="1000000000" />
73 <param name="minMapQuality" type="integer" label="minimum alternative mapping quality" value="35" /> 50 <param name="minMapQuality" type="integer" label="minimum alternative mapping quality" value="35" />
74 <param name="minReadDepth" type="integer" label="minimum number of read pairs required to establish a connection" value="2" /> 51 <param name="minReadDepth" type="integer" label="minimum number of read pairs required to establish a connection" value="2" />
75 <param name="maxHaploidCov" type="integer" label="maximum threshold of haploid sequence coverage for regions to be ignored" value="1000" /> 52 <param name="maxHaploidCov" type="integer" label="maximum threshold of haploid sequence coverage for regions to be ignored" value="1000" />
83 <data name="outputRawFile" format="tabular" /> 60 <data name="outputRawFile" format="tabular" />
84 <data name="outputVcfFile" format="vcf" /> 61 <data name="outputVcfFile" format="vcf" />
85 </outputs> 62 </outputs>
86 63
87 <help> 64 <help>
88 help 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.
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.
67 BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs.
68 Please read our paper for detailed algorithmic description. http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html
69
70 The input is a set of map files produced by a front-end aligner such as MAQ, BWA, NovoAlign and Bfast
71
72 The output format
73 ----------------------
74 BreakDancer's output file consists of the following columns:
75
76 1. Chromosome 1
77 2. Position 1
78 3. Orientation 1
79 4. Chromosome 2
80 5. Position 2
81 6. Orientation 2
82 7. Type of a SV
83 8. Size of a SV
84 9. Confidence Score
85 10. Total number of supporting read pairs
86 11. Total number of supporting read pairs from each map file
87 12. Estimated allele frequency
88 13. Software version
89 14. The run parameters
89 </help> 90 </help>
90 </tool> 91 </tool>