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comparison varscan/varscan_processSomatic.xml @ 0:848f3dc54593 draft

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author geert-vandeweyer
date Fri, 07 Mar 2014 06:17:32 -0500
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1 <tool id="varscan_processSomatic" name="ProcessSomatic" version="2.3.5">
2 <description>
3 Extract HC calls from Somatic Caller
4 </description>
5 <requirements>
6 <requirement type="package" version="2.3.5">VarScan</requirement>
7 </requirements>
8 <command interpreter="perl">
9
10 varscan_processSomatic.pl
11 "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar processSomatic"
12 "INPUT::$input"
13 "LOG::$log"
14
15 "OPTION::--min-tumor-freq $min_tumor_freq"
16 "OPTION::--max-normal-freq $max_normal_freq"
17 "OPTION::--p-value $p_value"
18 "OUTPUT::--loh $loh"
19 "OUTPUT::--loh_hc $loh_hc"
20 "OUTPUT::--germ $germ"
21 "OUTPUT::--germ_hc $germ_hc"
22 "OUTPUT::--som $som"
23 "OUTPUT::--som_hc $som_hc"
24 "OUTPUT::--som_hc_vcf $som_hc_vcf"
25 "OUTPUT::--germ_hc_vcf $germ_hc_vcf"
26 "OUTPUT::--loh_hc_vcf $loh_hc_vcf"
27
28 </command>
29
30 <inputs>
31
32 <param name="input" type="data" format="txt" label="Input File" help="VarScan Somatics output file in native format" />
33
34 <param name="min_tumor_freq" type="float" label="min-tumor-freq" help="Minimum variant allele frequency in tumor" optional="true" value="0.10"/>
35 <param name="max_normal_freq" type="float" label="max-normal-freq" help="Maximum variant allele frequency in normal" optional="true" value="0.05"/>
36 <param name="p_value" type="text" label="p-value" help="P-value for high-confidence calling" optional="true" value="0.07"/>
37 <param name="outtype" type="select" label="Output Type:" default="1">
38 <option value="0">Native VarScan Tables</option>
39 <option value="1">VCF format (only High Confidence)</option>
40 <option value="2">Both</option>
41 </param>
42
43 </inputs>
44 <outputs>
45 <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) " />
46 <data type="data" format="txt" name="loh" label="${tool.name} result on ${on_string} (loh) " >
47 <filter>outtype != "1"</filter>
48 </data>
49 <data type="data" format="txt" name="loh_hc" label="${tool.name} result on ${on_string} (loh_hc)">
50 <filter>outtype != "1"</filter>
51 </data>
52
53 <data type="data" format="txt" name="germ" label="${tool.name} result on ${on_string} (germline)" >
54 <filter>outtype != "1"</filter>
55 </data>
56
57 <data type="data" format="txt" name="germ_hc" label="${tool.name} result on ${on_string} (germline_hc)">
58 <filter>outtype != "1"</filter>
59 </data>
60
61 <data type="data" format="txt" name="som" label="${tool.name} result on ${on_string} (somatic)" >
62 <filter>outtype != "1"</filter>
63 </data>
64
65 <data type="data" format="txt" name="som_hc" label="${tool.name} result on ${on_string} (somatic_hc)" >
66 <filter>outtype != "1"</filter>
67 </data>
68
69 <data type="data" format="vcf" name="som_hc_vcf" label="${tool.name} result on ${on_string} (Somatic_HC.vcf)" >
70 <filter>outtype != "0"</filter>
71 </data>
72
73 <data type="data" format="vcf" name="loh_hc_vcf" label="${tool.name} result on ${on_string} (LOH_HC.vcf)" >
74 <filter>outtype != "0"</filter>
75 </data>
76
77 <data type="data" format="vcf" name="germ_hc_vcf" label="${tool.name} result on ${on_string} (Germline_HC.vcf)" >
78 <filter>outtype != "0"</filter>
79 </data>
80
81
82
83
84 </outputs>
85
86 <help>
87
88 .. class:: infomark
89
90 **What it does**
91
92 ::
93
94 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:
95
96 Germline variants (SNPs an dindels) in individual samples or pools of samples.
97 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
98 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
99 Somatic copy number alterations (CNAs) in tumor-normal exome data.
100
101
102 **Input**
103
104 ::
105
106 mpileup normal file - The SAMtools mpileup file for normal
107 mpileup tumor file - The SAMtools mpileup file for tumor
108
109
110 **Parameters**
111
112 ::
113
114 min-coverage
115 Minimum read depth at a position to make a call [8]
116
117 min-coverage-normal
118 Minimum coverage in normal to call somatic [8]
119
120 min-coverage-tumor
121 Minimum coverage in tumor to call somatic [6]
122
123 min-var-freq
124 Minimum variant frequency to call a heterozygote [0.10]
125
126 min-freq-for-hom
127 Minimum frequency to call homozygote [0.75]
128
129 normal-purity
130 Estimated purity (non-tumor content) of normal sample [1.00]
131
132 tumor-purity
133 Estimated purity (tumor content) of tumor sample [1.00]
134
135 p-value
136 Default p-value threshold for calling variants [0.99]
137
138 somatic-p-value
139 P-value threshold to call a somatic site [0.05]
140
141 strand-filter
142 If set to 1, removes variants with >90% strand bias
143
144 validation
145 If set to 1, outputs all compared positions even if non-variant
146
147 output-vcf
148 If set to 1, outputs in VCF format [Default]
149
150
151
152 </help>
153 </tool>
154