X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/76e8998d9326da7d99bcf083bd7234d62c2af63c..refs/heads/16377-test-check:/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 c1c9123a59..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. -
~$ arv keep put GenomeAnalysisTK-2.6-4.tar.bz2
+
~$ arv-put GenomeAnalysisTK-2.6-4.tar.bz2
 c905c8d8443a9c44274d98b7c6cfaa32+94