Mercurial > repos > jjohnson > pileup_to_vcf

diff pileup_to_vcf.xml @ 2:d6de2d1f4af9

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Fix read depth reporting
author Jim Johnson <jj@umn.edu>
date Sun, 03 Mar 2013 20:38:43 -0600
parents 3890f8ba0e4d
children fafa105e5f58
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--- a/pileup_to_vcf.xml	Mon Feb 18 19:11:47 2013 -0600
+++ b/pileup_to_vcf.xml	Sun Mar 03 20:38:43 2013 -0600
@@ -60,9 +60,10 @@
            help="Multiple alleles may be output in the VCF if the allowable frequency is below 0.5, otherwise only one will be reported"/>
     <param name="snps_only" type="boolean" truevalue="-s" falsevalue="" chacked="false" label="Only report SNPs, not indels" />
     <param name="depth_as" type="select" label="Report DP and SAF with read coverage of" help="The reported read voverage depth: DP, and the calculation of specific allele frequency (SAF) of variants">
-      <option value="ref" selected="true">Reads at this position</option>
+      <option value="source">Read coverage reported in pileup</option>
+      <option value="ref" selected="true">Reads at this position that have a base call</option>
       <option value="qual">Reads at this position taht pass the base call quality threshold</option>
-      <option value="all"></option>
+      <option value="all">All reads and indels</option>
     </param>
   </inputs>
   <outputs>