Updated README.md

README.md

@@ -1,6 +1,6 @@
 # FACETS.app
 
-## Version 0.9.2 (2015.08.02)
+## Version 0.9.3 (2015.08.11)
 
 Wrapper script which takes a tumor/normal BAM pair then
 
@@ -12,6 +12,20 @@ Wrapper script which takes a tumor/normal BAM pair then
 
 usage::
 ```bash
-    ./FACETS.app/run.sh NORMAL.BAM TUMOR.BAM
+
+usage:: FACETS/App.sh NORMALBAM TUMORBAM
+   or:: FACETS/App.sh NORMALBAM TUMORBAM TAG -c 50
+
+Arguments after TAG are passed to doFacets.R
 ```
 
+## Updates
+
+* run.sh no longer recounts if counts files already present; can call it to re-run facets instead of calling doFacets.R directly. 
+
+* ```--ndepth``` (```-n```) option added to ```doFacets.R``` added: reduction to 25 recommended by Venkat for high sensitivity
+
+* Waterfall supression from A. Penson
+
+The tumor depth and allele counts are normalized to remove the dependence of the log-ratio on normal depth, using a lowess fit. This is designed to remove the "waterfall" effect produced when degraded tumor DNA with small fragment size means that SNPs adjacent to target exons are consistently covered less well in the tumor than in the normal.
+