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comparison varscan_somatic.xml @ 2:51969e284317 draft default tip

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author fcaramia
date Thu, 20 Jun 2013 00:00:22 -0400
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1 <tool id="varscan_somatic" name="VarScan Somatic" version="2.3.5">
2 <description>
3 somatic mutation caller for cancer genomics
4 </description>
5 <requirements>
6 <requirement type="package" version="2.3.5">VarScan</requirement>
7 </requirements>
8 <command interpreter="perl">
9 varscan_somatic.pl
10 "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic"
11 "NORMAL::$normal"
12 "TUMOR::$tumor"
13 "OUTPUT::$output"
14
15 "OPTION::--min-coverage $min_coverage"
16 "OPTION::--min-coverage-normal $min_coverage_normal"
17 "OPTION::--min-coverage-tumor $min_coverage_tumor"
18
19 "OPTION::--min-var-freq $min_var_freq"
20 "OPTION::--min-freq-for-hom $min_freq_for_hom"
21
22 "OPTION::--normal-purity $normal_purity"
23 "OPTION::--tumor-purity $tumor_purity"
24
25 "OPTION::--p-value $p_value"
26 "OPTION::--somatic-p-value $somatic_p_value"
27
28 "OPTION::--strand-filter $strand_filter"
29 "OPTION::--validation $validation"
30 "OPTION::--output-vcf 1"
31
32
33
34 </command>
35
36 <inputs>
37
38 <param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
39 <param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
40
41 <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
42 <param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
43 <param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
44
45 <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
46 <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
47
48 <param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
49 <param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
50
51
52 <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
53 <param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
54
55 <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
56 <param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
57
58 </inputs>
59 <outputs>
60 <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
61 </outputs>
62
63 <help>
64
65 .. class:: infomark
66
67 **What it does**
68
69 ::
70
71 VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation:
72
73 Germline variants (SNPs an dindels) in individual samples or pools of samples.
74 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
75 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
76 Somatic copy number alterations (CNAs) in tumor-normal exome data.
77
78
79 **Input**
80
81 ::
82
83 mpileup normal file - The SAMtools mpileup file for normal
84 mpileup tumor file - The SAMtools mpileup file for tumor
85
86
87 **Parameters**
88
89 ::
90
91 min-coverage
92 Minimum read depth at a position to make a call [8]
93
94 min-coverage-normal
95 Minimum coverage in normal to call somatic [8]
96
97 min-coverage-tumor
98 Minimum coverage in tumor to call somatic [6]
99
100 min-var-freq
101 Minimum variant frequency to call a heterozygote [0.10]
102
103 min-freq-for-hom
104 Minimum frequency to call homozygote [0.75]
105
106 normal-purity
107 Estimated purity (non-tumor content) of normal sample [1.00]
108
109 tumor-purity
110 Estimated purity (tumor content) of tumor sample [1.00]
111
112 p-value
113 Default p-value threshold for calling variants [0.99]
114
115 somatic-p-value
116 P-value threshold to call a somatic site [0.05]
117
118 strand-filter
119 If set to 1, removes variants with >90% strand bias
120
121 validation
122 If set to 1, outputs all compared positions even if non-variant
123
124 output-vcf
125 If set to 1, outputs in VCF format [Default]
126
127
128
129 </help>
130 </tool>
131