Update README.md

added all --SV optionsto the manual

README.md

@@ -83,43 +83,53 @@ The reference is required for analysing cram files.
 
 NOTE: It is important that you use the TIDDIT.py wrapper for SV detection. The TIDDIT binary in the TIDDIT/bin folder does not perform any clustering, it simply extract SV signatures into a tab file.
 
-TIDDIT may be fine tuned by altering these optional parameters:
-	-o O	     output prefix(default=output)
-	-i I         paired reads maximum allowed insert size. Pairs aligning
-                     on the same chr at a distance higher than this are
-                     considered candidates for SV (default= 99.9th percentile
-                     of insert size)
-  -d D               expected reads orientations, possible values "innie" (->
-                     <-) or "outtie" (<- ->). Default: major orientation
-                     within the dataset
-  -p P               Minimum number of supporting pairs in order to call a
-                     variation event (default 3)
-  -r R               Minimum number of supporting split reads to call a small
-                     variant (default 3)
-  -q Q               Minimum mapping quality to consider an alignment (default
-                     5)
-  -Q Q               Minimum regional mapping quality (default 20)
-  -n N               the ploidy of the organism,(default = 2)
-  -e E               clustering distance parameter, discordant pairs closer
-                     than this distance are considered to belong to the same
-                     variant(default = sqrt(insert-size*2)*12)
-  -l L               min-pts parameter (default=3),must be set >= 2
-  -s S               Number of reads to sample when computing library
-                     statistics(default=25000000)
-  -z Z               minimum variant size (default=100), variants smaller than
-                     this will not be printed ( z < 10 is not recomended)
-  --force_ploidy     force the ploidy to be set to -n across the entire genome
-                     (i.e skip coverage normalisation of chromosomes)
-  --no_cluster       Run only the TIDDIT signal extraction
-  --debug            rerun the tiddit clustering procedure
-  --n_mask N_MASK    exclude regions from coverage calculation if they contain
-                     more than this fraction of N (default = 0.5)
-  --ref REF          reference fasta, used for GC correction and for reading
-                     cram
-  --p_ratio P_RATIO  minimum discordant pair/normal pair ratio at the
-                     breakpoint junction(default=0.2)
-  --r_ratio R_RATIO  minimum split read/coverage ratio at the breakpoint
-                     junction(default=0.1)
+
+TIDDIT may be fine-tuned by altering these optional parameters:
+
+	-o	output prefix(default=output)
+
+	-i	paired reads maximum allowed insert size. Pairs aligning
+		on the same chr at a distance higher than this are
+		considered candidates for SV (default= 99.9th percentile of insert size)
+		
+	-d	expected reads orientations, possible values "innie" (-> <-) or "outtie" (<- ->). 
+		Default: major orientation within the dataset
+		
+	-p	Minimum number of supporting pairs in order to call a variation event (default 3)
+
+	-r	Minimum number of supporting split reads to call a small variant (default 3)
+
+	-q	Minimum mapping quality to consider an alignment (default= 5)
+
+	-Q	Minimum regional mapping quality (default 20)
+
+	-n	the ploidy of the organism,(default = 2)
+
+	-e	clustering distance parameter, discordant pairs closer
+		than this distance are considered to belong to the same
+		variant(default = sqrt(insert-size*2)*12)
+		     
+	-l	min-pts parameter (default=3),must be set >= 2
+
+	-s	Number of reads to sample when computing library statistics(default=25000000)
+		     
+	-z	minimum variant size (default=100), variants smaller than
+		this will not be printed ( z < 10 is not recomended)
+		     
+	--force_ploidy	force the ploidy to be set to -n across the entire genome
+			(i.e skip coverage normalisation of chromosomes)
+		     
+	--no_cluster	Run only the TIDDIT signal extraction
+
+	--debug		rerun the tiddit clustering procedure
+
+	--n_mask	exclude regions from coverage calculation if they contain more than this fraction of N (default = 0.5)
+		     
+	--ref		reference fasta, used for GC correction and for reading cram
+		     
+	--p_ratio	minimum discordant pair/normal pair ratio at the breakpoint junction(default=0.2)
+		     
+	--r_ratio	minimum split read/coverage ratio at the breakpoint junction(default=0.1)