|
0
|
1 <tool id="polyphen2_web" name="PolyPhen-2 Webservice">
|
|
|
2 <description>Compute functional impact of SNVs </description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="4.1.0">beautifulsoup4</requirement>
|
|
|
5 <requirement type="python-module">bs4</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command interpreter="python">
|
|
|
8 polyphen2_web.py --ucscdb $ucscdb
|
|
|
9 --model $model
|
|
|
10 --filter $filter
|
|
|
11 --function $function
|
|
|
12 --input $input
|
|
|
13 --log $log_file
|
|
|
14 --full $full_file
|
|
|
15 --short $short_file
|
|
|
16 --snp $snp_file
|
|
|
17 </command>
|
|
|
18 <inputs>
|
|
|
19 <param format="txt" name="input" type="data" label="Variants File" />
|
|
|
20 <param name="ucscdb" type="select" label="Genome Assembly">
|
|
|
21 <option value="hg19">GRCh37/hg19</option>
|
|
|
22 <option value="hg18">NCBI36/hg18</option>
|
|
|
23 </param>
|
|
|
24 <param name="model" type="select" label="Classifier Model">
|
|
|
25 <option value="HumDiv">HumDiv</option>
|
|
|
26 <option value="HumVar">HumVar</option>
|
|
|
27 </param>
|
|
|
28 <param name="filter" type="select" label="Transcripts">
|
|
|
29 <option value="All">All</option>
|
|
|
30 <option value="Canonical">Canonical</option>
|
|
|
31 <option value="CCDS">CCDS</option>
|
|
|
32 </param>
|
|
|
33 <param name="function" type="select" label="Annotations">
|
|
|
34 <option value="c">Canonical</option>
|
|
|
35 <option value="m">CCDS</option>
|
|
|
36 <option value="All">All</option>
|
|
|
37 </param>
|
|
|
38 </inputs>
|
|
|
39 <outputs>
|
|
|
40 <data format="tabular" name="log_file" label="${tool.name} on ${on_string}: log" />
|
|
|
41 <data format="tabular" name="full_file" label="${tool.name} on ${on_string}: full"/>
|
|
|
42 <data format="tabular" name="short_file" label="${tool.name} on ${on_string}: short"/>
|
|
|
43 <data format="tabular" name="snp_file" label="${tool.name} on ${on_string}: snp"/>
|
|
|
44 </outputs>
|
|
|
45
|
|
|
46 <tests>
|
|
|
47 <test>
|
|
|
48 <param name="input" value="polyphen2_input.txt"/>
|
|
|
49 <param name="ucscdb" value="hg19"/>
|
|
|
50 <param name="model" value="HumDiv"/>
|
|
|
51 <param name="filter" value="All"/>
|
|
|
52 <param name="function" value="All"/>
|
|
|
53 <output name="log_file" file="polyphen2_log.txt"/>
|
|
|
54 <output name="full_file" file="polyphen2_full.txt"/>
|
|
|
55 <output name="short_file" file="polyphen2_short.txt"/>
|
|
|
56 <output name="snp_file" file="polyphen2_snp.txt"/>
|
|
|
57 </test>
|
|
3
|
58 <test>
|
|
|
59 <param name="input" value="polyphen_input.txt"/>
|
|
|
60 <param name="ucscdb" value="hg19"/>
|
|
|
61 <param name="model" value="HumDiv"/>
|
|
|
62 <param name="filter" value="All"/>
|
|
|
63 <param name="function" value="All"/>
|
|
|
64 <output name="log_file" file="polyphen_output_log.tsv"/>
|
|
|
65 <output name="full_file" file="polyphen_output_full.tsv"/>
|
|
|
66 <output name="short_file" file="polyphen_output_short.tsv"/>
|
|
|
67 <output name="snp_file" file="polyphen_output_snp.tsv"/>
|
|
|
68 </test>
|
|
|
69
|
|
0
|
70 </tests>
|
|
|
71 <help>
|
|
|
72 **What it does**
|
|
|
73 This tool interacts with the Web Version of Polyphen2 hosted at http://genetics.bwh.harvard.edu/pph2/
|
|
|
74
|
|
|
75 PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions
|
|
|
76 on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.
|
|
|
77
|
|
|
78 .. class:: infomark
|
|
|
79
|
|
2
|
80 *Classifier model* used by the probabilistic predictor:
|
|
|
81
|
|
|
82 -HumDiv is preferred for evaluating rare alleles, dense mapping of regions identified by genome-wide association studies,
|
|
|
83 and analysis of natural selection. HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions
|
|
|
84
|
|
|
85
|
|
|
86 -HumVar is better suited for diagnostics of Mendelian diseases which requires distinguishing mutations with drastic effects
|
|
|
87 from all the remaining human variation, including abundant mildly deleterious alleles.
|
|
|
88 HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions
|
|
0
|
89
|
|
|
90 .. class:: infomark
|
|
|
91
|
|
2
|
92 *Transcripts* A set of Transcripts on which genomic SNPs will be mapped:
|
|
|
93
|
|
|
94
|
|
|
95 -*All* includes all UCSC knownGene transcripts (highly redundant)
|
|
|
96
|
|
|
97 -*Canonical* includes UCSC knownCanonical subset
|
|
|
98
|
|
|
99 -*CCDS* further restricts knownCanonical subset to those transcripts which are also annotated as part of NCBI CCDS.
|
|
|
100
|
|
|
101
|
|
|
102 .. class:: infomark
|
|
|
103
|
|
|
104 *Annotations* for the following functional categories of genomic SNPs will be included in the output:
|
|
|
105
|
|
|
106
|
|
|
107 -*All*: coding-synon, introns, nonsense missense utr-3, utr-5.
|
|
|
108
|
|
|
109
|
|
|
110 -*Coding*: coding-synon, nonsense. missense
|
|
|
111
|
|
|
112
|
|
|
113 -*Missense*: missense.
|
|
|
114
|
|
|
115
|
|
|
116
|
|
|
117 .. class:: warningmark
|
|
|
118
|
|
|
119 Note that PolyPhen-2 predictions are always produced for missense
|
|
|
120
|
|
0
|
121
|
|
|
122 .. class:: infomark
|
|
|
123
|
|
|
124
|
|
2
|
125 Input format:
|
|
0
|
126
|
|
|
127
|
|
|
128 chr22:30421786 A/T
|
|
|
129
|
|
|
130 chr22:29446079 A/G
|
|
|
131
|
|
|
132 chr22:40814500 A/G
|
|
|
133
|
|
|
134 chr22:40815256 C/T
|
|
|
135
|
|
|
136
|
|
2
|
137
|
|
0
|
138 **Citations**
|
|
|
139
|
|
|
140 If you use this tool please cite:
|
|
|
141
|
|
|
142 Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010).
|
|
|
143 "A method and server for predicting damaging missense mutations."
|
|
|
144
|
|
|
145 </help>
|
|
|
146 </tool>
|
|
|
147
|
|
|
148
|
|
|
149
|
|
|
150
|
|
|
151
|
|
|
152
|
|
|
153
|
