readme update. v0.5.5

BilkentCompGen · Sep 27, 2018 · 3c88f56 · 3c88f56
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Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/Makefile b/Makefile
@@ -1,5 +1,5 @@
 TARDIS_VERSION := "0.5.5"
-TARDIS_UPDATE := "September 26, 2018"
+TARDIS_UPDATE := "September 27, 2018"
 TARDIS_DEBUG := 0
 BUILD_DATE := "$(shell date)"
 CC=gcc

diff --git a/README.md b/README.md
@@ -74,7 +74,7 @@ Running TARDIS - QUICK mode
 Running TARDIS - SENSITIVE mode (mrFAST Mappings)
 =================================================
 
-Sensitive mode uses mrFast mappings (all possible mappings) with read-pair and read-depth signatures. This mode can detect Deletions, Insertions, Inversions, Mobile Element Insertions and Tandem Duplications.
+Sensitive mode uses mrFAST mappings (all possible mappings) with read-pair and read-depth signatures. 
 
  tardis -i myinput.bam --ref human_g1k_v37.fasta --sonic human_g1k_v37.sonic \
   --sensitive --out myoutput
@@ -92,8 +92,12 @@ All parameters
  --out [output prefix] : Prefix for the output file names.
  --ref [reference genome] : Reference genome in FASTA format.
  --sonic [sonic file] : SONIC file that contains assembly annotations.
+ --read-count [int] : # of clusters that a specific read can be involved in (Default is 10).
  --mei ["Alu:L1:SVA"] : List of mobile element names.
  --no-soft-clip : Skip soft clip remapping.
+ --no-interdup : Skip interspersed duplication clustering.
+ --resolved : Output sequence resolved vcf calls.
+ --xa : Look for the alternative mapping locations in BWA.
  --first-chr [chr_index] : Start running from a specific chromosome [index in ref]
  --last-chr [chr_index] : Run up to a specific chromosome [index in ref]
 

diff --git a/sonic b/sonic