diff --git a/doc/ReadQualityRecalibrator/README b/doc/ReadQualityRecalibrator/README
new file mode 100644
index 000000000..97c7f3b12
--- /dev/null
+++ b/doc/ReadQualityRecalibrator/README
@@ -0,0 +1,90 @@
+Read Quality Recalibrator
+-------------------------
+The tools in this package recalibrate quality scores 
+assigned to nucleic acids in an aligned BAM file by 
+analyzing the covariation between machine reported 
+quality scores and: 
+
+1) the position within the read, and 
+2) the preceding nucleotide (sequencing chemistry effect).  
+
+The aligned reads have their dbSNP sites masked out, and 
+the mismatched bases are used as a metric for the true error 
+rate of the system.  The error rate at different dinucleotides 
+and positions in the read is then fed into a logistic regression 
+system which outputs a correction factor for each of those 
+combinations which are then use to output a recalibrated BAM 
+file. 
+
+Software Dependencies
+---------------------
+The recalibrator currently depends on the following
+applications.  Please install these before proceeding.
+
+- Java Runtime Environment 1.6.0_12 or later
+- Python 2.4.2 or later
+- R 2.6.0 or later
+- samtools 0.1.4 or later.
+
+Please update the file paths at the top of 
+RecalQual.py to point to the local installations of the
+software listed above.
+
+Running
+-------
+Before running the tool, please update the file paths
+listed at the top of RecalQual.py to point to the
+local installations of the tools listed above.
+
+The recalibrator has two modes: recalibration and
+evaluation, which can be run separately or jointly.
+By default, the recalibrator will recalibrate only.
+
+To calibrate a given bam file, run the following 
+command:
+
+python RecalQual.py <source bam> <recalibrated bam>
+
+After recalibration, performing evaluation will walk 
+through the source BAM file again, remeasuring the 
+differences between empirical vs. reported quality.  
+The results of evaluation are comma-delimited text 
+files (.csv) and graphs (.png) which can be found 
+in the output directory (see below) for the given run.
+A successful recalibration should produce a plot of 
+empirical vs. observed qualities that shows little
+difference between the two values.
+
+To both recalibrate and evaluate, execute:
+
+python RecalQual.py --recalibrate --evaluate <source bam> <recalibrated bam>
+
+To (only) evaluate a given bam file after calibrating:
+
+python RecalQual.py --evaluate <source bam> <recalibrated bam>
+
+Output
+------
+The recalibration process keeps many incremental
+files around for future analysis.  By default, all 
+of these files will be grouped into the directory 
+'output.<source bam>/'.  By default, this directory
+will be created within the working directory.  This
+location can be changed by editing the output_root
+variable at the top of RecalQual.py.
+
+It is safe to delete this supplemental output 
+directory at any time.
+
+Known Issues
+------------
+- The recalibrator places severe memory demands on
+  files with large numbers of read groups (> 1000).
+- If running in 'evaluation' mode (see the 'Running'
+  section above), X11 is required to generate the 
+  graphs.  If running on a machine via ssh, be certain
+  to enable X tunnelling.
+
+Support
+-------
+For support, please email gsadevelopers@broad.mit.edu.