Mercurial > repos > jjohnson > gatk2

diff reduce_reads.xml @ 11:5faf7ace8aee draft

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Add HaplotypeCaller
author Jim Johnson <jj@umn.edu>
date Thu, 08 Nov 2012 10:38:18 -0600
parents a14e79e7ac75
children d73c92a7b0ea
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line diff
--- a/reduce_reads.xml	Tue Nov 06 12:07:36 2012 -0600
+++ b/reduce_reads.xml	Thu Nov 08 10:38:18 2012 -0600
@@ -123,7 +123,12 @@
     #end if
   </command>
   <inputs>
-    <param name="input_recal" type="data" format="csv" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" />
+    <param name="input_recal" type="data" format="csv" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" >
+      <help>The input covariates table file which enables on-the-fly base quality score recalibration. 
+            Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. 
+            Please be aware that one should only run recalibration with the covariates file created on the same input bam(s).
+      </help>
+    </param>
     <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
         <option value="cached">Locally cached</option>