---
layout: default
navsection: userguide
title: "Using GATK with Arvados"
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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.
{% include 'tutorial_expectations' %}
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>
c905c8d8443a9c44274d98b7c6cfaa32+94
</code></pre>
</notextile>
Next, you need the GATK Resource Bundle[2]. This may already be available in Arvados. If not, you will need to download the files listed below and put them into Keep.
<notextile>
<pre><code>~$ <span class="userinput">arv keep ls -s d237a90bae3870b3b033aea1e99de4a9+10820</span>
50342 1000G_omni2.5.b37.vcf.gz
1 1000G_omni2.5.b37.vcf.gz.md5
464 1000G_omni2.5.b37.vcf.idx.gz
1 1000G_omni2.5.b37.vcf.idx.gz.md5
43981 1000G_phase1.indels.b37.vcf.gz
1 1000G_phase1.indels.b37.vcf.gz.md5
326 1000G_phase1.indels.b37.vcf.idx.gz
1 1000G_phase1.indels.b37.vcf.idx.gz.md5
537210 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.gz
1 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.gz.md5
3473 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz
1 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz.md5
19403 Mills_and_1000G_gold_standard.indels.b37.vcf.gz
1 Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5
536 Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz
1 Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz.md5
29291 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz
1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz.md5
565 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz
1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz.md5
37930 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz
1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz.md5
592 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz
1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz.md5
5898484 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam
112 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz
1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz.md5
1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.md5
3837 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz
1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz.md5
65 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz
1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz.md5
275757 dbsnp_137.b37.excluding_sites_after_129.vcf.gz
1 dbsnp_137.b37.excluding_sites_after_129.vcf.gz.md5
3735 dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz
1 dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz.md5
998153 dbsnp_137.b37.vcf.gz
1 dbsnp_137.b37.vcf.gz.md5
3890 dbsnp_137.b37.vcf.idx.gz
1 dbsnp_137.b37.vcf.idx.gz.md5
58418 hapmap_3.3.b37.vcf.gz
1 hapmap_3.3.b37.vcf.gz.md5
999 hapmap_3.3.b37.vcf.idx.gz
1 hapmap_3.3.b37.vcf.idx.gz.md5
3 human_g1k_v37.dict.gz
1 human_g1k_v37.dict.gz.md5
2 human_g1k_v37.fasta.fai.gz
1 human_g1k_v37.fasta.fai.gz.md5
849537 human_g1k_v37.fasta.gz
1 human_g1k_v37.fasta.gz.md5
1 human_g1k_v37.stats.gz
1 human_g1k_v37.stats.gz.md5
3 human_g1k_v37_decoy.dict.gz
1 human_g1k_v37_decoy.dict.gz.md5
2 human_g1k_v37_decoy.fasta.fai.gz
1 human_g1k_v37_decoy.fasta.fai.gz.md5
858592 human_g1k_v37_decoy.fasta.gz
1 human_g1k_v37_decoy.fasta.gz.md5
1 human_g1k_v37_decoy.stats.gz
1 human_g1k_v37_decoy.stats.gz.md5
</code></pre>
</notextile>
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.
<notextile>
<pre><code>~$ <span class="userinput">src_version=76588bfc57f33ea1b36b82ca7187f465b73b4ca4</span>
~$ <span class="userinput">vcf_input=5ee633fe2569d2a42dd81b07490d5d13+82</span>
~$ <span class="userinput">gatk_binary=c905c8d8443a9c44274d98b7c6cfaa32+94</span>
~$ <span class="userinput">gatk_bundle=d237a90bae3870b3b033aea1e99de4a9+10820</span>
~$ <span class="userinput">cat >the_job <<EOF
{
"script":"GATK2-VariantFiltration",
"repository":"arvados",
"script_version":"$src_version",
"script_parameters":
{
"input":"$vcf_input",
"gatk_binary_tarball":"$gatk_binary",
"gatk_bundle":"$gatk_bundle"
}
}
EOF</span>
</code></pre>
</notextile>
* @"input"@ is collection containing the source VCF data. Here we are using an exome report from PGP participant hu34D5B9.
* @"gatk_binary_tarball"@ is a Keep collection containing the GATK 2 binary distribution[1] tar file.
* @"gatk_bundle"@ is a Keep collection containing the GATK resource bundle[2].
Now start a job:
<notextile>
<pre><code>~$ <span class="userinput">arv job create --job "$(cat the_job)"</span>
{
"href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4",
"kind":"arvados#job",
"etag":"9j99n1feoxw3az448f8ises12",
"uuid":"qr1hi-8i9sb-n9k7qyp7bs5b9d4",
"owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
"created_at":"2013-12-17T19:02:15Z",
"modified_by_client_uuid":"qr1hi-ozdt8-obw7foaks3qjyej",
"modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
"modified_at":"2013-12-17T19:02:15Z",
"updated_at":"2013-12-17T19:02:15Z",
"submit_id":null,
"priority":null,
"script":"GATK2-VariantFiltration",
"script_parameters":{
"input":"5ee633fe2569d2a42dd81b07490d5d13+82",
"gatk_binary_tarball":"c905c8d8443a9c44274d98b7c6cfaa32+94",
"gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820"
},
"script_version":"76588bfc57f33ea1b36b82ca7187f465b73b4ca4",
"cancelled_at":null,
"cancelled_by_client_uuid":null,
"cancelled_by_user_uuid":null,
"started_at":null,
"finished_at":null,
"output":null,
"success":null,
"running":null,
"is_locked_by_uuid":null,
"log":null,
"runtime_constraints":{},
"tasks_summary":{},
"dependencies":[
"5ee633fe2569d2a42dd81b07490d5d13+82",
"c905c8d8443a9c44274d98b7c6cfaa32+94",
"d237a90bae3870b3b033aea1e99de4a9+10820"
]
}
</code></pre>
</notextile>
Once the job completes, the output can be found in hu34D5B9-exome-filtered.vcf:
<notextile><pre><code>~$ <span class="userinput">arv keep ls bedd6ff56b3ae9f90d873b1fcb72f9a3+91</span>
hu34D5B9-exome-filtered.vcf
</code></pre>
</notextile>
h2. Notes
fn1. "Download the GATK tools":http://www.broadinstitute.org/gatk/download
fn2. "Information about the GATK resource bundle":http://gatkforums.broadinstitute.org/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it and "direct download link":ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.5/b37/ (if prompted, submit an empty password)