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author nilesh
date Fri, 12 Jul 2013 15:21:36 -0500
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1 <tool id="somatic_sniper_tool" name="Somatic Sniper" version="1.0.2">
2 <description>: identify single nucleotide positions that are different between tumor and normal</description>
3 <requirements>
4 <requirement type="package" version="1.0.0">somatic-sniper</requirement>
5 </requirements>
6 <command interpreter="perl">
7 somatic_sniper_wrapper.pl
8
9 "NORMAL::$normal"
10 "TUMOR::$tumor"
11 "OUTPUT::$snp_output"
12 "OPTION::-F $output"
13
14 #if $option.option == "modify_parameters":
15 "OPTION::-q $option.readFilter"
16 "OPTION::-Q $option.somaticFilter"
17 "OPTION::-s $option.mutationPrior"
18 #if str($option.disablePriors) == "true"
19 "OPTION::-p"
20 #end if
21 #end if
22
23 "OPTION::-f $reference.fields.path"
24
25
26 </command>
27 <inputs>
28 <param name="reference" type="select" label="Select a reference genome">
29 <options from_data_table="all_fasta">
30 <filter type="sort_by" column="2" />
31 <validator type="no_options" message="No indexes are available" />
32 </options>
33 </param>
34
35 <param format="bam" name="normal" type="data" label="Normal sample" help=""/>
36 <param format="bam" name="tumor" type="data" label="Tumor Sample" help=""/>
37 <param name="output" type="select" label="Output Type" help="" optional="true">
38 <option value="classic" selected="true">Classic</option>
39 <option value="vcf">VCF</option>
40 <option value="bed">BED</option>
41 </param>
42
43
44 <conditional name="option">
45 <param name="option" type="select" label="Optional Parameters" help="" optional="true">
46 <option value="default_parameters" selected="true">Default Parameters</option>
47 <option value="modify_parameters">Modify Parameters</option>
48 </param>
49 <when value="modify_parameters">
50
51 <param name="readFilter" label="filtering reads with mapping quality less than" type="integer" value="0" optional="true" />
52 <param name="somaticFilter" label="filtering somatic snv output with somatic quality less than" type="integer" value="15" optional="true" />
53 <param name="disablePriors" type="select" label="disable priors in the somatic calculation. Increases sensitivity for solid tumors" help="" optional="true">
54 <option value="true" >true</option>
55 <option value="false" selected="true">false</option>
56 </param>
57 <param name="mutationPrior" label="prior probability of a somatic mutation" type="float" value="0.10000" optional="true" />
58
59 </when>
60
61 </conditional>
62
63 </inputs>
64 <outputs>
65 <data name="snp_output" format="text" label="${tool.name} result on ${on_string}" />
66 </outputs>
67 <help>
68 |
69
70
71 **Reference**
72
73 http://gmt.genome.wustl.edu/somatic-sniper/current/
74
75 -----
76
77 **What it does**
78
79 The purpose of this program is to identify single nucleotide positions that are different between tumor and normal
80 (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the
81 differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood
82 model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are
83 different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255)
84 that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and
85 255 means there is a probability of 1 – 10(255/-10) that the genotypes are different between tumor and normal. This is consistent
86 with how the SAM format reports such probabilities.
87
88 bam-somaticsniper [options] -f ref.fasta tumor.bam normal.bam snp_output_file
89
90 Bam files must contain LB tag in @RG line.
91 Picard tools can be used to add lines to BAM headers.
92
93 -----
94
95 **Required Parameters**
96
97 ::
98
99 -f FILE REQUIRED reference sequence in the FASTA format
100
101 -----
102
103 **Options**
104
105 ::
106
107 -q INT filtering reads with mapping quality less than INT [0]
108
109 -Q INT filtering somatic snv output with somatic quality less than INT [15]
110
111 -p FLAG disable priors in the somatic calculation. Increases sensitivity for solid tumors
112
113 -J FLAG Use prior probabilities accounting for the somatic mutation rate
114
115 -s FLOAT prior probability of a somatic mutation (implies -J) [0.010000]
116
117 -T FLOAT theta in maq consensus calling model (for -c/-g) [0.850000]
118
119 -N INT number of haplotypes in the sample (for -c/-g) [2]
120
121 -r FLOAT prior of a difference between two haplotypes (for -c/-g) [0.001000]
122
123 -F STRING select output format [classic]
124 Available formats:
125 classic
126 vcf
127 bed
128
129 -----
130
131 **File Formats**
132
133 ::
134
135 Classic:
136
137 Each line contains the following tab-separated values:
138
139 1. Chromosome
140 2. Position
141 3. Reference base
142 4. IUB genotype of tumor
143 5. IUB genotype of normal
144 6. Somatic Score
145 7. Tumor Consensus quality
146 8. Tumor variant allele quality
147 9. Tumor mean mapping quality
148 10. Normal Consensus quality
149 11. Normal variant allele quality
150 12. Normal mean mapping quality
151 13. Depth in tumor (# of reads crossing the position)
152 14. Depth in normal (# of reads crossing the position)
153 15. Mean base quality of reads supporting reference in tumor
154 16. Mean mapping quality of reads supporting reference in tumor
155 17. Depth of reads supporting reference in tumor
156 18. Mean base quality of reads supporting variant(s) in tumor
157 19. Mean mapping quality of reads supporting variant(s) in tumor
158 20. Depth of reads supporting variant(s) in tumor
159 21. Mean base quality of reads supporting reference in normal
160 22. Mean mapping quality of reads supporting reference in normal
161 23. Depth of reads supporting reference in normal
162 24. Mean base quality of reads supporting variant(s) in normal
163 25. Mean mapping quality of reads supporting variant(s) in normal
164 26. Depth of reads supporting variant(s) in normal
165
166
167
168 </help>
169 </tool>
170
171