This page shows you how to set up and start using Google Genomics.
Before you begin
- If you don't already have one, sign up for a Google Account.
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Sign in to your Google account.
If you don't already have one, sign up for a new account.
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In the Cloud Platform Console, go to the Projects page and create a new project.
- Enable billing for your project.
- Enable the Genomics, BigQuery, and Cloud Storage APIs.
Launch Cloud Shell to use the command line
You can use Cloud Shell to access the Google Cloud SDK, which includes tools and libraries that you need to create and manage resources on Google Cloud Platform, including Google Genomics, Google Compute Engine, Google Cloud Storage, and BigQuery.
To launch Cloud Shell:
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Navigate to the project you want to use in the Cloud Platform Console.
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Click the Activate Google Cloud Shell button at the top of the console window.
A Cloud Shell session opens inside a new frame at the bottom of the console and displays a command-line prompt.
Run a query
Query a dataset from the 1000 Genomes Project using the Genomics tools.
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Search a variant set for variants at a specific location:
gcloud alpha genomics variants list --variant-set-id "10473108253681171589" --reference-name "22" --start 51003835 --end 51003836
This query returns the following variant:
VARIANT_SET_ID REFERENCE_NAME START END REFERENCE_BASES ALTERNATE_BASES 10473108253681171589 22 51003835 51003836 A [u'G']
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Search callsets for individuals with calls (including reference calls) at the same location:
gcloud alpha genomics callsets list "10473108253681171589" --limit 10
This query returns the following individuals:
ID NAME VARIANT_SET_IDS 10473108253681171589-0 HG00261 [u'10473108253681171589'] 10473108253681171589-1 HG00593 [u'10473108253681171589'] 10473108253681171589-2 NA12749 [u'10473108253681171589'] 10473108253681171589-3 HG00150 [u'10473108253681171589'] 10473108253681171589-4 NA19675 [u'10473108253681171589'] 10473108253681171589-5 NA19651 [u'10473108253681171589'] 10473108253681171589-6 NA19393 [u'10473108253681171589'] 10473108253681171589-7 NA19207 [u'10473108253681171589'] 10473108253681171589-8 HG00342 [u'10473108253681171589'] 10473108253681171589-9 NA12546 [u'10473108253681171589']
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Gives the details of the calls at this location.
gcloud alpha genomics variants list --variant-set-id "10473108253681171589" --reference-name "22" --start 51003835 --end 51003836 --format json
This query returns the following details:
[ { "alternateBases": [ "G" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "HG00261", "genotype": [ 1, 1 ], "genotypeLikelihood": [ -5.0, -1.2, -0.03 ], ...
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You can also search read group sets:
gcloud alpha genomics readgroupsets list 10473108253681171589 --limit 5
This query returns the following 10 read group set IDs:
ID NAME REFERENCE_SET_ID CMvnhpKTFhDq9e2Yy9G-Bg HG02573 EOSt9JOVhp3jkwE CMvnhpKTFhCEmf_d_o_JCQ HG03894 EOSt9JOVhp3jkwE CMvnhpKTFhCjz9_25e_lCw HG01440 EOSt9JOVhp3jkwE CMvnhpKTFhCKwY-lmoOYDQ NA20790 EOSt9JOVhp3jkwE CMvnhpKTFhCYnZrehsCAFg HG01455 EOSt9JOVhp3jkwE CMvnhpKTFhDv55POyoCXIw NA19074 EOSt9JOVhp3jkwE CMvnhpKTFhDVt4WpxI2KJw HG01794 EOSt9JOVhp3jkwE CMvnhpKTFhDt6uGJ6YSOLQ HG02166 EOSt9JOVhp3jkwE CMvnhpKTFhDC-oi_l9fLMw HG03268 EOSt9JOVhp3jkwE CMvnhpKTFhCPqeCAnfPLNA HG04014 EOSt9JOVhp3jkwE
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Get the description of a read group set:
gcloud alpha genomics readgroupsets describe CMvnhpKTFhDq9e2Yy9G-Bg
This query returns the following description:
datasetId: '10473108253681171589' filename: HG02573.mapped.ILLUMINA.bwa.GWD.low_coverage.20130415.bam id: CMvnhpKTFhDq9e2Yy9G-Bg info: SAM:@SQ: - "SN:1\tLN:249250621\tAS:NCBI37\tM5:1b22b98cdeb4a9304cb5d48026a85128\tSP:Human\t\ UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz" ...
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Search a set of read group set IDs, and give a genomic range to query:
gcloud alpha genomics reads list "CJ_ppJ-WCxDxrtDr5fGIhBA" --reference-name "chr20" --start 68198 --end 69000 --limit 5
This query returns the following description:
REFERENCE_NAME POSITION REVERSE_STRAND FRAGMENT_NAME SEQUENCE chr20 68099 True H7F3RADXX_1:1:1207:2208623:0 CTTACAGTTCTACGGGATAATAGCTTATCTCATAAGGCCTCAGCTTTCTTTAATAATTTCTAGAAGCAGACGTTATTGTGTCATGCACACTAAGTGTTGC │ chr20 68106 True H7F3RADXX_1:1:2202:1444084:0 AGTTCTATTGGATAATAGCTTATCTCATAAGGCCTCAGCTTTCTTTAATAATTTCTAGAAGCAGACGTTATTGTGTCATGCACACTCAGTGTTGCAAATT │ chr20 68109 True H7F3RADXX_1:1:2210:379591:0 TACGGGATAATAGCTTATCTCATAAGGCCTCAGCTTTCTTTAATAATTTCTAGAAGCAGACGTTATTGTGTCATGCACACTCAGTGTTGCAAATTAATGG chr20 68110 False H7F3RADXX_1:1:2206:641983:0 ACGGGATAATAGCTTATCTCATAAGGCCTCAGCTTTCTTTAATAATTTCTAGAAGCAGACGTTATTGTGTCATGCACACTCAGTGTTGCAAATTAATGGT chr20 68112 True H7F4RADXX_0:2:2111:1926421:0 GGGATAATAGCTTATCTCATAAGGCCTCAGCTTTCTTTAATAATTTCTAGAAGCAGACGTTATTGTGTCATGCACACTCAGTGTTGCAAATTAATGGTCT
What's next
- Try Analyzing Variants with BigQuery.
- Install the Cloud SDK and Genomics Commands.
- To perform common genomics tasks on Google Cloud Platform, view the tutorials on Read the Docs.
- To manage genomic data, you can use Google's implementation of the standard defined by the Global Alliance for Genomics and Health. For more information, see Definitions for the Genomics API.
- Join the discussion about Google Genomics.