This page shows you how to run a pipeline that uses the Cloud Genomics Pipelines API to create an index file (BAI file) from a large binary file containing DNA sequences (BAM file).

Before you begin

  1. Sign in to your Google Account.

    If you don't already have one, sign up for a new account.

  2. In the GCP Console, go to the Manage resources page and select or create a project.

    Go to the Manage resources page

  3. Make sure that billing is enabled for your Google Cloud Platform project.

    Learn how to enable billing

  4. Enable the Cloud Genomics, Compute Engine, and Cloud Storage JSON APIs.

    Enable the APIs

  5. Install and initialize the Cloud SDK.
  6. Alternatively, you can use Google Cloud Shell, which comes with the Cloud SDK already installed.

Run the pipeline

  1. Create a BUCKET environment variable. The variable points to a Cloud Storage bucket that uses your project name with -genomics appended.

    export BUCKET=gs://PROJECT_ID-genomics
  2. Create the bucket using the gsutil mb command:

    gsutil mb ${BUCKET}
  3. Run a pipeline using the gcloud command-line tool, providing a BAM file as the input and a BAI file as the output. The pipeline invokes the Pipelines API, creates a Compute Engine VM instance, and then runs the pipeline process on the instance. After the process finishes, the instance is automatically shut down and the BAI file is copied to your Cloud Storage bucket.

    gcloud alpha genomics pipelines run \
        --regions us-east1 \
        --command-line 'samtools index ${BAM} ${BAI}' \
        --docker-image "gcr.io/genomics-tools/samtools" \
        --inputs BAM=gs://genomics-public-data/NA12878.chr20.sample.bam \
        --outputs BAI=${BUCKET}/NA12878.chr20.sample.bam.bai

    If successful, the command returns the following:

    Running [projects/PROJECT_ID/operations/OPERATION_ID]
  4. The pipeline will take a few minutes to finish. You can run the following command to track its status. Replace OPERATION_ID with the value printed in the previous step.

    gcloud alpha genomics operations wait OPERATION_ID

    After the operation finishes, it prints the following message:

    Waiting for [projects/PROJECT_ID/operations/OPERATION_ID]...done.
  5. Verify that the BAI file was generated:

    gsutil ls ${BUCKET}

    The command should return the following:


You've just run a pipeline using the Pipelines API to create a BAI file from a BAM file.

Clean up

  1. Use the gsutil rm command to delete the BAI file:

    gsutil rm ${BUCKET}/NA12878.chr20.sample.bam.bai
  2. If you created the bucket specifically for this quickstart and no longer need it, delete it using the gsutil rb command:

    gsutil rb ${BUCKET}

What's next

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