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comparison varscan_somatic.xml @ 2:90c9b7a6e58b draft

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author geert-vandeweyer
date Fri, 07 Mar 2014 06:18:29 -0500
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1:e5831cc9185f 2:90c9b7a6e58b
1 <tool id="varscan_somatic" name="VarScan Somatic (VCF Output)" 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
10 varscan_somatic.pl
11 "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic"
12 "NORMAL::$normal"
13 "TUMOR::$tumor"
14 "TUMORBAM::$tumorbam"
15 "OUTPUT::$output"
16 "LOG::$log"
17
18 "OPTION::--min-coverage $min_coverage"
19 "OPTION::--min-coverage-normal $min_coverage_normal"
20 "OPTION::--min-coverage-tumor $min_coverage_tumor"
21
22 "OPTION::--min-var-freq $min_var_freq"
23 "OPTION::--min-freq-for-hom $min_freq_for_hom"
24
25 "OPTION::--normal-purity $normal_purity"
26 "OPTION::--tumor-purity $tumor_purity"
27
28 "OPTION::--p-value $p_value"
29 "OPTION::--somatic-p-value $somatic_p_value"
30
31 "OPTION::--strand-filter $strand_filter"
32 "OPTION::--validation $validation"
33 "OPTION::--output-vcf 1"
34
35
36
37 </command>
38
39 <inputs>
40
41 <param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
42 <param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
43 <param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" />
44
45 <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
46 <param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
47 <param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
48
49 <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
50 <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
51
52 <param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
53 <param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
54
55
56 <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
57 <param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
58
59 <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
60 <param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
61
62 </inputs>
63 <outputs>
64 <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
65 <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
66 <!--<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP file)" />
67 <data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL file)" />-->
68
69
70 </outputs>
71
72 <help>
73
74 .. class:: infomark
75
76 **What it does**
77
78 ::
79
80 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:
81
82 Germline variants (SNPs an dindels) in individual samples or pools of samples.
83 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
84 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
85 Somatic copy number alterations (CNAs) in tumor-normal exome data.
86
87
88 **Input**
89
90 ::
91
92 mpileup normal file - The SAMtools mpileup file for normal
93 mpileup tumor file - The SAMtools mpileup file for tumor
94
95
96 **Parameters**
97
98 ::
99
100 min-coverage
101 Minimum read depth at a position to make a call [8]
102
103 min-coverage-normal
104 Minimum coverage in normal to call somatic [8]
105
106 min-coverage-tumor
107 Minimum coverage in tumor to call somatic [6]
108
109 min-var-freq
110 Minimum variant frequency to call a heterozygote [0.10]
111
112 min-freq-for-hom
113 Minimum frequency to call homozygote [0.75]
114
115 normal-purity
116 Estimated purity (non-tumor content) of normal sample [1.00]
117
118 tumor-purity
119 Estimated purity (tumor content) of tumor sample [1.00]
120
121 p-value
122 Default p-value threshold for calling variants [0.99]
123
124 somatic-p-value
125 P-value threshold to call a somatic site [0.05]
126
127 strand-filter
128 If set to 1, removes variants with >90% strand bias
129
130 validation
131 If set to 1, outputs all compared positions even if non-variant
132
133 output-vcf
134 If set to 1, outputs in VCF format [Default]
135
136
137
138 </help>
139 </tool>
140