annotate somatic_sniper.xml @ 3:4308fb6335c4 draft

Uploaded
author nilesh
date Fri, 28 Jun 2013 16:26:19 -0400
parents be1edd8c72b7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
1 <tool id="somatic_sniper_tool" name="Somatic Sniper" version="1.0.2">
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
2 <description>: identify single nucleotide positions that are different between tumor and normal</description>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
3 <requirements>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
4 <requirement type="package" version="unstable">somatic-sniper</requirement>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
5 </requirements>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
6 <command interpreter="perl">
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
7 somatic_sniper_wrapper.pl
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
8
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
9 "NORMAL::$normal"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
10 "TUMOR::$tumor"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
11 "OUTPUT::$snp_output"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
12 "OPTION::-F $output"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
13
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
14 #if $option.option == "modify_parameters":
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
15 "OPTION::-q $option.readFilter"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
16 "OPTION::-Q $option.somaticFilter"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
17 "OPTION::-s $option.mutationPrior"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
18 #if str($option.disablePriors) == "true"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
19 "OPTION::-p"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
20 #end if
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
21 #end if
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
22
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
23 "OPTION::-f $reference.fields.path"
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
24
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
25
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
26 </command>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
27 <inputs>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
28 <param name="reference" type="select" label="Select a reference genome">
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
29 <options from_data_table="all_fasta">
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
30 <filter type="sort_by" column="2" />
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
31 <validator type="no_options" message="No indexes are available" />
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
32 </options>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
33 </param>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
34
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
35 <param format="bam" name="normal" type="data" label="Normal sample" help=""/>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
36 <param format="bam" name="tumor" type="data" label="Tumor Sample" help=""/>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
37 <param name="output" type="select" label="Output Type" help="" optional="true">
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
38 <option value="classic" selected="true">Classic</option>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
39 <option value="vcf">VCF</option>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
40 <option value="bed">BED</option>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
41 </param>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
42
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
43
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
44 <conditional name="option">
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
45 <param name="option" type="select" label="Optional Parameters" help="" optional="true">
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
46 <option value="default_parameters" selected="true">Default Parameters</option>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
47 <option value="modify_parameters">Modify Parameters</option>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
48 </param>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
49 <when value="modify_parameters">
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
50
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
51 <param name="readFilter" label="filtering reads with mapping quality less than" type="integer" value="0" optional="true" />
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
52 <param name="somaticFilter" label="filtering somatic snv output with somatic quality less than" type="integer" value="15" optional="true" />
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
53 <param name="disablePriors" type="select" label="disable priors in the somatic calculation. Increases sensitivity for solid tumors" help="" optional="true">
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
54 <option value="true" >true</option>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
55 <option value="false" selected="true">false</option>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
56 </param>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
57 <param name="mutationPrior" label="prior probability of a somatic mutation" type="float" value="0.10000" optional="true" />
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
58
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
59 </when>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
60
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
61 </conditional>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
62
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
63 </inputs>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
64 <outputs>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
65 <data name="snp_output" format="text" label="${tool.name} result on ${on_string}" />
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
66 </outputs>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
67 <help>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
68 |
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
69
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
70
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
71 **Reference**
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
72
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
73 http://gmt.genome.wustl.edu/somatic-sniper/current/
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
74
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
75 -----
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
76
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
77 **What it does**
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
78
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
79 The purpose of this program is to identify single nucleotide positions that are different between tumor and normal
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
80 (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
81 differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
82 model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
83 different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255)
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
84 that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
85 255 means there is a probability of 1 – 10(255/-10) that the genotypes are different between tumor and normal. This is consistent
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
86 with how the SAM format reports such probabilities.
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
87
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
88 bam-somaticsniper [options] -f ref.fasta tumor.bam normal.bam snp_output_file
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
89
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
90 Bam files must contain LB tag in @RG line.
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
91 Picard tools can be used to add lines to BAM headers.
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
92
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
93 -----
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
94
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
95 **Required Parameters**
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
96
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
97 ::
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
98
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
99 -f FILE REQUIRED reference sequence in the FASTA format
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
100
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
101 -----
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
102
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
103 **Options**
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
104
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
105 ::
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
106
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
107 -q INT filtering reads with mapping quality less than INT [0]
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
108
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
109 -Q INT filtering somatic snv output with somatic quality less than INT [15]
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
110
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
111 -p FLAG disable priors in the somatic calculation. Increases sensitivity for solid tumors
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
112
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
113 -J FLAG Use prior probabilities accounting for the somatic mutation rate
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
114
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
115 -s FLOAT prior probability of a somatic mutation (implies -J) [0.010000]
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
116
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
117 -T FLOAT theta in maq consensus calling model (for -c/-g) [0.850000]
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
118
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
119 -N INT number of haplotypes in the sample (for -c/-g) [2]
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
120
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
121 -r FLOAT prior of a difference between two haplotypes (for -c/-g) [0.001000]
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
122
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
123 -F STRING select output format [classic]
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
124 Available formats:
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
125 classic
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
126 vcf
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
127 bed
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
128
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
129 -----
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
130
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
131 **File Formats**
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
132
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
133 ::
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
134
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
135 Classic:
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
136
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
137 Each line contains the following tab-separated values:
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
138
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
139 1. Chromosome
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
140 2. Position
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
141 3. Reference base
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
142 4. IUB genotype of tumor
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
143 5. IUB genotype of normal
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
144 6. Somatic Score
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
145 7. Tumor Consensus quality
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
146 8. Tumor variant allele quality
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
147 9. Tumor mean mapping quality
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
148 10. Normal Consensus quality
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
149 11. Normal variant allele quality
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
150 12. Normal mean mapping quality
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
151 13. Depth in tumor (# of reads crossing the position)
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
152 14. Depth in normal (# of reads crossing the position)
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
153 15. Mean base quality of reads supporting reference in tumor
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
154 16. Mean mapping quality of reads supporting reference in tumor
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
155 17. Depth of reads supporting reference in tumor
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
156 18. Mean base quality of reads supporting variant(s) in tumor
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
157 19. Mean mapping quality of reads supporting variant(s) in tumor
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
158 20. Depth of reads supporting variant(s) in tumor
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
159 21. Mean base quality of reads supporting reference in normal
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
160 22. Mean mapping quality of reads supporting reference in normal
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
161 23. Depth of reads supporting reference in normal
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
162 24. Mean base quality of reads supporting variant(s) in normal
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
163 25. Mean mapping quality of reads supporting variant(s) in normal
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
164 26. Depth of reads supporting variant(s) in normal
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
165
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
166
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
167
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
168 </help>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
169 </tool>
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
170
be1edd8c72b7 Uploaded
nilesh
parents:
diff changeset
171