From a003874ff2443202ec7601627f0cb322d4baea7d Mon Sep 17 00:00:00 2001 From: "Nicholas D. Socci" Date: Tue, 11 Aug 2015 20:16:54 -0400 Subject: [PATCH] Updated README.md --- README.md | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ad8f50b..c9fa66f 100644 --- a/README.md +++ b/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. +