# HG changeset patch
# User p.lucas
# Date 1644497204 0
# Node ID 0179feb477d7fc1cfd3ec0fd74e3f37f88a3bd1b
# Parent  cad99097cdc2829e1a21f076be21dfbcf0e641fa
Uploaded

diff -r cad99097cdc2 -r 0179feb477d7 varscan_readcount.xml
--- a/varscan_readcount.xml	Thu Feb 10 12:39:08 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 12:46:44 2022 +0000
@@ -16,9 +16,14 @@
   </outputs>
   <help>
     USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS
+
     OPTIONS:
+
       --output-file   Output file to contain the readcounts
+
       --min-coverage  Minimum read depth at a position to make a call (default: 1)
+
       --min-base-qual Minimum base quality at a position to count a read (default: 20)
+
   </help>
 </tool>