Mercurial > repos > fcaramia > somatic_sniper

changeset 2:0bf1ebd2dadd draft

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Deleted selected files
author fcaramia
date Wed, 19 Jun 2013 02:47:58 -0400
parents 3cfcd9d2eba4
children d71c18eab8e3
files somatic_sniper.xml
diffstat 1 files changed, 0 insertions(+), 172 deletions(-) [+]
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--- a/somatic_sniper.xml	Wed Jun 19 02:47:44 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,172 +0,0 @@
-<tool id="somatic_sniper_tool" name="Somatic Sniper" version="1.0.2">
-  <description>: identify single nucleotide positions that are different between tumor and normal</description>
-  <requirements>
-    <requirement type="package" version="0.1.6">samtools</requirement>
-    <requirement type="package" version="unstable">somatic-sniper</requirement>	
-  </requirements>
-  <command interpreter="perl">
-  	somatic_sniper_wrapper.pl
-
-  	"NORMAL::$normal"
-  	"TUMOR::$tumor"
-	"OUTPUT::$snp_output"
-  	"OPTION::-F $output"
-  	
-  	 #if $option.option == "modify_parameters":
-  	 	"OPTION::-q $option.readFilter"
-  	 	"OPTION::-Q $option.somaticFilter"
-  	 	"OPTION::-s $option.mutationPrior"
-  	 	#if str($option.disablePriors) == "true" 
-  	 		"OPTION::-p"  	 	  	 	
- 		#end if
-  	 #end if
-  	
-  	"OPTION::-f $reference.fields.path"  	
-	
-
-  </command>
-	<inputs>
-	<param name="reference" type="select" label="Select a reference genome">
-		<options from_data_table="all_fasta">
-			<filter type="sort_by" column="2" />
-			<validator type="no_options" message="No indexes are available" />
-		</options>
-	</param>
-
-	<param format="bam" name="normal" type="data" label="Normal sample" help=""/>
-	<param format="bam" name="tumor" type="data" label="Tumor Sample" help=""/>
-	<param name="output" type="select" label="Output Type" help="" optional="true">
-		<option value="classic" selected="true">Classic</option>
-		<option value="vcf">VCF</option>
-		<option value="bed">BED</option>
-	</param>
-
-
-	<conditional name="option">
-		<param name="option" type="select" label="Optional Parameters" help="" optional="true">
-			<option value="default_parameters" selected="true">Default Parameters</option>
-			<option value="modify_parameters">Modify Parameters</option>
-		</param>
-		<when value="modify_parameters">
-	
-			<param name="readFilter" label="filtering reads with mapping quality less than"  type="integer" value="0" optional="true" />
-			<param name="somaticFilter" label="filtering somatic snv output with somatic quality less than"  type="integer" value="15" optional="true" />
-			<param name="disablePriors" type="select" label="disable priors in the somatic calculation. Increases sensitivity for solid tumors" help="" optional="true">
-				<option value="true"  >true</option>
-				<option value="false" selected="true">false</option>
-			</param>
-			<param name="mutationPrior"  label="prior probability of a somatic mutation" type="float" value="0.10000" optional="true" />
-      
-		</when>
-		
-	</conditional>
-
-	</inputs>
-	<outputs>
-		<data name="snp_output" format="text" label="${tool.name} result on ${on_string}" />
-	</outputs>
-	<help>
-|
-
-
-**Reference**
-	
-  http://gmt.genome.wustl.edu/somatic-sniper/current/
-  
------
-
-**What it does**
-
-The purpose of this program is to identify single nucleotide positions that are different between tumor and normal 
-(or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the 
-differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood 
-model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are 
-different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255) 
-that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and 
-255 means there is a probability of 1 – 10(255/-10) that the genotypes are different between tumor and normal. This is consistent 
-with how the SAM format reports such probabilities. 
-
-bam-somaticsniper [options] -f ref.fasta tumor.bam normal.bam snp_output_file
-
-Bam files must contain LB tag in @RG line.
-Picard tools can be used to add lines to BAM headers.
-
------
- 
-**Required Parameters**
-
-::
-
-  -f 	FILE REQUIRED reference sequence in the FASTA format
-
------
-
-**Options**
-
-::
-
- -q 	INT    filtering reads with mapping quality less than INT [0]
- 
- -Q	INT    filtering somatic snv output with somatic quality less than  INT [15]
-        
- -p 	FLAG   disable priors in the somatic calculation. Increases sensitivity for solid tumors
-        
- -J 	FLAG   Use prior probabilities accounting for the somatic mutation rate
- 
- -s 	FLOAT  prior probability of a somatic mutation (implies -J) [0.010000]
-        
- -T 	FLOAT  theta in maq consensus calling model (for -c/-g) [0.850000]
-        
- -N 	INT    number of haplotypes in the sample (for -c/-g) [2]
-        
- -r 	FLOAT  prior of a difference between two haplotypes (for -c/-g) [0.001000]
-        
- -F 	STRING select output format [classic]
-        Available formats:
-        	classic
-        	vcf
-        	bed
-             
------            
-
-**File Formats**      
-             
-::
-
-  Classic:
-
-  Each line contains the following tab-separated values:
-
-    1. Chromosome
-    2. Position
-    3. Reference base
-    4. IUB genotype of tumor
-    5. IUB genotype of normal
-    6. Somatic Score
-    7. Tumor Consensus quality
-    8. Tumor variant allele quality
-    9. Tumor mean mapping quality
-    10. Normal Consensus quality
-    11. Normal variant allele quality
-    12. Normal mean mapping quality
-    13. Depth in tumor (# of reads crossing the position)
-    14. Depth in normal (# of reads crossing the position)
-    15. Mean base quality of reads supporting reference in tumor
-    16. Mean mapping quality of reads supporting reference in tumor
-    17. Depth of reads supporting reference in tumor
-    18. Mean base quality of reads supporting variant(s) in tumor
-    19. Mean mapping quality of reads supporting variant(s) in tumor
-    20. Depth of reads supporting variant(s) in tumor
-    21. Mean base quality of reads supporting reference in normal
-    22. Mean mapping quality of reads supporting reference in normal
-    23. Depth of reads supporting reference in normal
-    24. Mean base quality of reads supporting variant(s) in normal
-    25. Mean mapping quality of reads supporting variant(s) in normal
-    26. Depth of reads supporting variant(s) in normal
-
-
-
-	</help>
-</tool>
-
-