X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ad76f76cdd557d61497aa0ff26e0537788f2d5b6..c59af50bc2f7a366cd12a8dd6fc7d7e3b1c32480:/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid

diff --git a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
index bf9b24272c..544ccbd35e 100644
--- a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+++ b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -3,6 +3,11 @@ layout: default
 navsection: userguide
 title: "Using GATK with Arvados"
 ...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
 
 This tutorial demonstrates how to use the Genome Analysis Toolkit (GATK) with Arvados. In this example we will install GATK and then create a VariantFiltration job to assign pass/fail scores to variants in a VCF file.
 
@@ -13,7 +18,7 @@ h2. Installing GATK
 Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
 
 <notextile>
-<pre><code>~$ <span class="userinput">arv keep put GenomeAnalysisTK-2.6-4.tar.bz2</span>
+<pre><code>~$ <span class="userinput">arv-put GenomeAnalysisTK-2.6-4.tar.bz2</span>
 c905c8d8443a9c44274d98b7c6cfaa32+94
 </code></pre>
 </notextile>
@@ -87,7 +92,7 @@ Next, you need the GATK Resource Bundle[2].  This may already be available in Ar
 
 h2. Submit a GATK job
 
-The Arvados distribution includes an example crunch script ("crunch_scripts/GATK2-VariantFiltration":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-VariantFiltration) that runs the GATK VariantFiltration tool with some default settings.
+The Arvados distribution includes an example crunch script ("crunch_scripts/GATK2-VariantFiltration":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-VariantFiltration) that runs the GATK VariantFiltration tool with some default settings.
 
 <notextile>
 <pre><code>~$ <span class="userinput">src_version=76588bfc57f33ea1b36b82ca7187f465b73b4ca4</span>