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comparison varscan/varscan_mpileup.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_mpileup" name="VarScan mpileup" version="2.3.5">
2 <description>
3 mutation caller for targeted, exome, and whole-genome resequencing
4 </description>
5 <requirements>
6 <requirement type="package" version="2.3.5">VarScan</requirement>
7 </requirements>
8 <command interpreter="perl">
9
10 varscan_mpileup.pl
11 "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar $exe_command"
12 "INPUT::$in_file"
13 "OUTPUT::$output"
14 "LOG::$log"
15 "OPTION::--min-coverage $min_coverage"
16 "OPTION::--min-reads2 $min_reads2"
17 "OPTION::--min-avg-qual $min_avg_qual"
18 "OPTION::--min-var-freq $min_var_freq"
19 "OPTION::--min-freq-for-hom $min_freq_for_hom"
20 "OPTION::--p-value $p_value"
21 "OPTION::--strand-filter $strand_filter"
22 "OPTION::--output-vcf 1"
23
24 #if ($vcf_sample_list):
25 "OPTION::--vcf-sample-list $vcf_sample_list"
26 #end if
27 "OPTION::--variants $variants"
28
29
30
31 </command>
32
33 <inputs>
34
35 <param name="exe_command" type="select" label="Command" help="" optional="false">
36 <option value="mpileup2snp" >mpileup2snp</option>
37 <option value="mpileup2indel">mpileup2indel</option>
38 <option value="mpileup2cns">mpileup2cns</option>
39 </param>
40 <param name="in_file" type="data" format="pileup" label="mpileup file" help="The SAMtools mpileup file" />
41 <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
42 <param name="min_reads2" type="integer" label="min-reads2" help="" optional="true" value="2"/>
43 <param name="min_avg_qual" type="integer" label="min-avg-qual" help="" optional="true" value="15"/>
44 <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.01"/>
45 <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
46 <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
47 <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
48 <param name="vcf_sample_list" type="data" label="vcf-sample-list" format="txt" help="" optional="true" />
49 <param name="variants" type="integer" label="variants" help="Set to 1 to report only variants" optional="true" value="1"/>
50
51
52 </inputs>
53 <outputs>
54 <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
55 <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
56 </outputs>
57
58 <help>
59
60 .. class:: infomark
61
62 **What it does**
63
64 ::
65
66 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:
67
68 Germline variants (SNPs an dindels) in individual samples or pools of samples.
69 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
70 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
71 Somatic copy number alterations (CNAs) in tumor-normal exome data.
72
73
74 **Input**
75
76 ::
77
78 mpileup file - The SAMtools mpileup file
79
80
81 **Parameters**
82
83 ::
84
85 commands
86 mpileup2snp Identify SNPs from an mpileup file
87 mpileup2indel Identify indels an mpileup file
88 mpileup2cns Call consensus and variants from an mpileup file
89
90 min-coverage
91 Minimum read depth at a position to make a call [8]
92
93 min-reads2
94 Minimum supporting reads at a position to call variants [2]
95
96 min-avg-qual
97 Minimum base quality at a position to count a read [15]
98
99 min-var-freq
100 Minimum variant allele frequency threshold [0.01]
101
102 min-freq-for-hom
103 Minimum frequency to call homozygote [0.75]
104
105 p-value
106 Default p-value threshold for calling variants [99e-02]
107
108 strand-filter
109 Ignore variants with >90% support on one strand [1]
110
111 output-vcf
112 If set to 1, outputs in VCF format
113
114 vcf-sample-list
115 For VCF output, a list of sample names in order, one per line
116
117 variants
118 Report only variant (SNP/indel) positions [0]
119
120
121
122 </help>
123 </tool>
124