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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:37:45 -0400
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1 <macros>
2 <xml name="morinlab_citation">
3 <citation type="bibtex">
4 @unpublished{
5 albuquerque2016galaxy,
6 author = "Marco Albuquerque and Bruno Grande and Elie Ritch and Martin Krzywinski and Prasath Pararajalingam and Selin Jessa and Paul Boutros and Sohrab Shah and Ryan Morin",
7 title = "A Suite of Galaxy Tools for Cancer Mutational Analysis",
8 note = "Unpublished Manuscript",
9 year = "2016"
10 }
11 </citation>
12 </xml>
13 <xml name="vardict_citation">
14 <citation type="bibtex">
15 @article{
16 Lai20062016,
17 title = {VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research},
18 author = {Lai, Zhongwu and Markovets, Aleksandra and Ahdesmaki, Miika and Chapman, Brad and Hofmann, Oliver and McEwen, Robert and Johnson, Justin and Dougherty, Brian and Barrett, J. Carl and Dry, Jonathan R.},
19 journal = {Nucleic Acids Research}
20 volume = {44},
21 number = {11},
22 pages = {e108},
23 year = {2016},
24 doi = {10.1093/nar/gkw227}
25 }
26 </citation>
27 </xml>
28 <xml name="somatic_sniper_citation">
29 <citation>
30 @article{
31 Larson01022012,
32 author = {Larson, David E. and Harris, Christopher C. and Chen, Ken and Koboldt, Daniel C. and Abbott, Travis E. and Dooling, David J. and Ley, Timothy J. and Mardis, Elaine R. and Wilson, Richard K. and Ding, Li},
33 title = {SomaticSniper: identification of somatic point mutations in whole genome sequencing data},
34 volume = {28},
35 number = {3},
36 pages = {311-317},
37 year = {2012},
38 doi = {10.1093/bioinformatics/btr665},
39 journal = {Bioinformatics}
40 }
41 </citation>
42 </xml>
43 <xml name="galaxy_citation">
44 <citation>
45 @ARTICLE{Goecks2010-ra,
46 title = "Galaxy: a comprehensive approach for supporting accessible,
47 reproducible, and transparent computational research in the life
48 sciences",
49 author = "Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and
50 {Galaxy Team}",
51 journal = "Genome Biol.",
52 volume = 11,
53 number = 8,
54 pages = "R86",
55 month = "25~",
56 year = 2010
57 }
58 </citation>
59 </xml>
60
61 <xml name="delly_citation">
62 <citation>
63 @ARTICLE{Rausch2012-yi,
64 title = "{DELLY}: structural variant discovery by integrated paired-end
65 and split-read analysis",
66 author = "Rausch, Tobias and Zichner, Thomas and Schlattl, Andreas and
67 St{\"{u}}tz, Adrian M and Benes, Vladimir and Korbel, Jan O",
68 journal = "Bioinformatics",
69 volume = 28,
70 number = 18,
71 pages = "i333--i339",
72 month = "15~",
73 year = 2012
74 }
75 </citation>
76 </xml>
77 <xml name="mutationseq_citation">
78 <citation type="bibtex">
79 @ARTICLE{Ding2012-jq,
80 title = "Feature-based classifiers for somatic mutation detection in
81 tumour-normal paired sequencing data",
82 author = "Ding, Jiarui and Bashashati, Ali and Roth, Andrew and Oloumi,
83 Arusha and Tse, Kane and Zeng, Thomas and Haffari, Gholamreza and
84 Hirst, Martin and Marra, Marco A and Condon, Anne and Aparicio,
85 Samuel and Shah, Sohrab P",
86 journal = "Bioinformatics",
87 volume = 28,
88 number = 2,
89 pages = "167--175",
90 month = "15~" # jan,
91 year = 2012
92 }
93 </citation>
94 </xml>
95
96 <xml name="strelka_citation">
97 <citation type="bibtex">
98 @ARTICLE{Saunders2012-nh,
99 title = "Strelka: accurate somatic small-variant calling from sequenced
100 tumor-normal sample pairs",
101 author = "Saunders, Christopher T and Wong, Wendy S W and Swamy, Sajani and
102 Becq, Jennifer and Murray, Lisa J and Cheetham, R Keira",
103 journal = "Bioinformatics",
104 volume = 28,
105 number = 14,
106 pages = "1811--1817",
107 month = "15~" # jul,
108 year = 2012
109 }
110 </citation>
111 </xml>
112 <xml name="radia_citation">
113 <citation type="bibtex">
114 @article{
115 Radenbaugh2014-tj,
116 title={RADIA: RNA and DNA integrated analysis for somatic
117 mutation detection},
118 author={Radenbaugh, Amie J and Ma, Singer and Ewing, Adam and Stuart,
119 Joshua M and Collisson, Eric A and Zhu, Jingchun and Haussler,
120 David},
121 journal={PLoS One},
122 volume={9},
123 number={11},
124 pages={e111516},
125 year={2014},
126 publisher={PLoS}
127 }
128 </citation>
129 </xml>
130 <xml name="titan_citation">
131 <citation type="bibtex">
132 @ARTICLE{Ha2014-pu,
133 title = "{TITAN}: inference of copy number architectures in clonal cell
134 populations from tumor whole-genome sequence data",
135 author = "Ha, Gavin and Roth, Andrew and Khattra, Jaswinder and Ho,
136 Julie and Yap, Damian and Prentice, Leah M and Melnyk,
137 Nataliya and McPherson, Andrew and Bashashati, Ali and Laks,
138 Emma and Biele, Justina and Ding, Jiarui and Le, Alan and
139 Rosner, Jamie and Shumansky, Karey and Marra, Marco A and
140 Gilks, C Blake and Huntsman, David G and McAlpine, Jessica N
141 and Aparicio, Samuel and Shah, Sohrab P",
142 journal = "Genome Res.",
143 publisher = "Cold Spring Harbor Lab",
144 volume = 24,
145 number = 11,
146 pages = "1881--1893",
147 month = "1~" # nov,
148 year = 2014,
149 keywords = "computational method"
150 }
151 </citation>
152 </xml>
153 </macros>