Merge branch 'master' into 2221-complete-docker
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1 ---
2 layout: default
3 navsection: userguide
4 navmenu: Tutorials
5 title: "Using GATK with Arvados"
6
7 ...
8
9 h1. Using GATK with Arvados
10
11 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.
12
13 *This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
14
15 h2. Installing GATK
16
17 Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":tutorial-keep.html.
18
19 <notextile>
20 <pre><code>~$ <span class="userinput">arv keep put GenomeAnalysisTK-2.6-4.tar.bz2</span>
21 c905c8d8443a9c44274d98b7c6cfaa32+94
22 </code></pre>
23 </notextile>
24
25 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.
26
27 <notextile>
28 <pre><code>~$ <span class="userinput">arv keep ls -s d237a90bae3870b3b033aea1e99de4a9+10820</span>
29   50342 1000G_omni2.5.b37.vcf.gz
30       1 1000G_omni2.5.b37.vcf.gz.md5
31     464 1000G_omni2.5.b37.vcf.idx.gz
32       1 1000G_omni2.5.b37.vcf.idx.gz.md5
33   43981 1000G_phase1.indels.b37.vcf.gz
34       1 1000G_phase1.indels.b37.vcf.gz.md5
35     326 1000G_phase1.indels.b37.vcf.idx.gz
36       1 1000G_phase1.indels.b37.vcf.idx.gz.md5
37  537210 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.gz
38       1 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.gz.md5
39    3473 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz
40       1 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz.md5
41   19403 Mills_and_1000G_gold_standard.indels.b37.vcf.gz
42       1 Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5
43     536 Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz
44       1 Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz.md5
45   29291 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz
46       1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz.md5
47     565 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz
48       1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz.md5
49   37930 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz
50       1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz.md5
51     592 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz
52       1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz.md5
53 5898484 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam
54     112 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz
55       1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz.md5
56       1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.md5
57    3837 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz
58       1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz.md5
59      65 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz
60       1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz.md5
61  275757 dbsnp_137.b37.excluding_sites_after_129.vcf.gz
62       1 dbsnp_137.b37.excluding_sites_after_129.vcf.gz.md5
63    3735 dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz
64       1 dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz.md5
65  998153 dbsnp_137.b37.vcf.gz
66       1 dbsnp_137.b37.vcf.gz.md5
67    3890 dbsnp_137.b37.vcf.idx.gz
68       1 dbsnp_137.b37.vcf.idx.gz.md5
69   58418 hapmap_3.3.b37.vcf.gz
70       1 hapmap_3.3.b37.vcf.gz.md5
71     999 hapmap_3.3.b37.vcf.idx.gz
72       1 hapmap_3.3.b37.vcf.idx.gz.md5
73       3 human_g1k_v37.dict.gz
74       1 human_g1k_v37.dict.gz.md5
75       2 human_g1k_v37.fasta.fai.gz
76       1 human_g1k_v37.fasta.fai.gz.md5
77  849537 human_g1k_v37.fasta.gz
78       1 human_g1k_v37.fasta.gz.md5
79       1 human_g1k_v37.stats.gz
80       1 human_g1k_v37.stats.gz.md5
81       3 human_g1k_v37_decoy.dict.gz
82       1 human_g1k_v37_decoy.dict.gz.md5
83       2 human_g1k_v37_decoy.fasta.fai.gz
84       1 human_g1k_v37_decoy.fasta.fai.gz.md5
85  858592 human_g1k_v37_decoy.fasta.gz
86       1 human_g1k_v37_decoy.fasta.gz.md5
87       1 human_g1k_v37_decoy.stats.gz
88       1 human_g1k_v37_decoy.stats.gz.md5
89 </code></pre>
90 </notextile>
91
92 h2. Submit a GATK job
93
94 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.
95
96 <notextile>
97 <pre><code>~$ <span class="userinput">src_version=76588bfc57f33ea1b36b82ca7187f465b73b4ca4</span>
98 ~$ <span class="userinput">vcf_input=5ee633fe2569d2a42dd81b07490d5d13+82</span>
99 ~$ <span class="userinput">gatk_binary=c905c8d8443a9c44274d98b7c6cfaa32+94</span>
100 ~$ <span class="userinput">gatk_bundle=d237a90bae3870b3b033aea1e99de4a9+10820</span>
101 ~$ <span class="userinput">cat &gt;the_job &lt;&lt;EOF
102 {
103  "script":"GATK2-VariantFiltration",
104  "script_version":"$src_version",
105  "script_parameters":
106  {
107   "input":"$vcf_input",
108   "gatk_binary_tarball":"$gatk_binary",
109   "gatk_bundle":"$gatk_bundle"
110  }
111 }
112 EOF</span>
113 </code></pre>
114 </notextile>
115
116 * @"input"@ is collection containing the source VCF data. Here we are using an exome report from PGP participant hu34D5B9.
117 * @"gatk_binary_tarball"@ is a Keep collection containing the GATK 2 binary distribution[1] tar file.
118 * @"gatk_bundle"@ is a Keep collection containing the GATK resource bundle[2].
119
120 Now start a job:
121
122 <notextile>
123 <pre><code>~$ <span class="userinput">arv job create --job "$(cat the_job)"</span>
124 {
125  "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4",
126  "kind":"arvados#job",
127  "etag":"9j99n1feoxw3az448f8ises12",
128  "uuid":"qr1hi-8i9sb-n9k7qyp7bs5b9d4",
129  "owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
130  "created_at":"2013-12-17T19:02:15Z",
131  "modified_by_client_uuid":"qr1hi-ozdt8-obw7foaks3qjyej",
132  "modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
133  "modified_at":"2013-12-17T19:02:15Z",
134  "updated_at":"2013-12-17T19:02:15Z",
135  "submit_id":null,
136  "priority":null,
137  "script":"GATK2-VariantFiltration",
138  "script_parameters":{
139   "input":"5ee633fe2569d2a42dd81b07490d5d13+82",
140   "gatk_binary_tarball":"c905c8d8443a9c44274d98b7c6cfaa32+94",
141   "gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820"
142  },
143  "script_version":"76588bfc57f33ea1b36b82ca7187f465b73b4ca4",
144  "cancelled_at":null,
145  "cancelled_by_client_uuid":null,
146  "cancelled_by_user_uuid":null,
147  "started_at":null,
148  "finished_at":null,
149  "output":null,
150  "success":null,
151  "running":null,
152  "is_locked_by_uuid":null,
153  "log":null,
154  "runtime_constraints":{},
155  "tasks_summary":{},
156  "dependencies":[
157   "5ee633fe2569d2a42dd81b07490d5d13+82",
158   "c905c8d8443a9c44274d98b7c6cfaa32+94",
159   "d237a90bae3870b3b033aea1e99de4a9+10820"
160  ],
161  "log_stream_href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4/log_tail_follow"
162 }
163 ~$ <span class="userinput">arv job log_tail_follow --uuid qr1hi-8i9sb-n9k7qyp7bs5b9d4</span>
164 Tue Dec 17 19:02:16 2013 salloc: Granted job allocation 1251
165 Tue Dec 17 19:02:17 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  check slurm allocation
166 Tue Dec 17 19:02:17 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  node compute13 - 8 slots
167 Tue Dec 17 19:02:17 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  start
168 Tue Dec 17 19:02:17 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  Install revision 76588bfc57f33ea1b36b82ca7187f465b73b4ca4
169 Tue Dec 17 19:02:18 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  Clean-work-dir exited 0
170 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  Install exited 0
171 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  script GATK2-VariantFiltration
172 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  script_version 76588bfc57f33ea1b36b82ca7187f465b73b4ca4
173 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  script_parameters {"input":"5ee633fe2569d2a42dd81b07490d5d13+82","gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820","gatk_binary_tarball":"c905c8d8443a9c44274d98b7c6cfaa32+94"}
174 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  runtime_constraints {"max_tasks_per_node":0}
175 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  start level 0
176 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 0 done, 0 running, 1 todo
177 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 job_task qr1hi-ot0gb-d3sjxerucfbvyev
178 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 child 4946 started on compute13.1
179 Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 0 done, 1 running, 0 todo
180 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 child 4946 on compute13.1 exit 0 signal 0 success=true
181 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 success in 1 seconds
182 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 output
183 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  wait for last 0 children to finish
184 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 1 done, 0 running, 1 todo
185 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  start level 1
186 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 1 done, 0 running, 1 todo
187 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 job_task qr1hi-ot0gb-w8ujbnulxjaamxf
188 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 child 4984 started on compute13.1
189 Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 1 done, 1 running, 0 todo
190 Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 child 4984 on compute13.1 exit 0 signal 0 success=true
191 Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 success in 110 seconds
192 Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 output bedd6ff56b3ae9f90d873b1fcb72f9a3+91
193 Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  wait for last 0 children to finish
194 Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 2 done, 0 running, 0 todo
195 Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  release job allocation
196 Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  Freeze not implemented
197 Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  collate
198 Tue Dec 17 19:04:10 2013 salloc: Job allocation 1251 has been revoked.
199 Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  output bedd6ff56b3ae9f90d873b1fcb72f9a3+91
200 Tue Dec 17 19:04:11 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  finish
201 Tue Dec 17 19:04:12 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  log manifest is 1e77aaceee2df499e14dc5dde5c3d328+91
202 </code></pre>
203 </notextile>
204
205 Once the job completes, the output can be found in hu34D5B9-exome-filtered.vcf:
206
207 <notextile><pre><code>~$ <span class="userinput">arv keep ls bedd6ff56b3ae9f90d873b1fcb72f9a3+91</span>
208 hu34D5B9-exome-filtered.vcf
209 </code></pre>
210 </notextile>
211
212 h2. Notes
213
214 fn1. "Download the GATK tools":http://www.broadinstitute.org/gatk/download
215
216 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)