Mercurial > repos > p.lucas > varscan_readcount

changeset 8:939dcf9b0374 draft

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add help
author p.lucas
date Thu, 10 Feb 2022 12:35:26 +0000
parents 2709a3c1548c
children 221cdb2901f3
files varscan_readcount.xml
diffstat 1 files changed, 7 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/varscan_readcount.xml	Thu Feb 10 12:34:34 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 12:35:26 2022 +0000
@@ -12,4 +12,11 @@
   <outputs>
     <data name="output" format="vcf"/>
   </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>