How-to guides

Tip: Using a higher level workflow specification can simplify implementing and managing the Cloud Life Sciences API. See Tutorials for examples of workflow specifications that have integrated with the Cloud Life Sciences API.

Getting started

• Getting started

  Set up your project and environment for Cloud Life Sciences.

API migration

• Migrating to Cloud Life Sciences v2beta

  Migrate to the new Cloud Life Sciences v2beta.

Analyzing variants with BigQuery

• Analyzing variants with BigQuery

  Use BigQuery to run fast SQL-like queries and interactively explore massive data sets.

• Running interval JOINs with BigQuery

  Use BigQuery to run JOIN queries on variants with data described by genomic region intervals.

Running the Variant Transforms tool

• Copying and storing genomic variants

  Copy and store raw VCF files in Cloud Storage.

• Storing and loading genomic variants

  Load and transform VCF files into BigQuery for large-scale analysis.

• Handling large inputs

  Learn how to improve performance and reduce costs when loading large numbers of files.

• Validating VCF files with the preprocessor tool

  Use the Variant Transforms tool VCF files preprocessor to validate VCF files.

• Parsing and annotating VCF files

  Use the annotation support available in the Variant Transforms tool.

• Understanding the BigQuery variants table schema

  Use the Cloud Life Sciences API to export variants to BigQuery.

• Flattening the BigQuery variants table

  Flatten the BigQuery variants table to remove repeated records.

• Troubleshooting the variant transforms tool

  Get solutions to common problems.

Reading data from Cloud Storage

• Reading data from Cloud Storage

  Use the Cloud Life Sciences implementation of the htsget protocol to read genomic data stored in Cloud Storage.

Logging

• Viewing Cloud Audit Logs

  View logs for Cloud Life Sciences operations.

Long-running operations

• Managing long-running operations

  Learn how to manage the lifecycle of long-running Cloud Life Sciences API operations.

Troubleshooting

• Troubleshooting and error messages

  See solutions to common issues encountered in Cloud Life Sciences.

Public datasets

• Public datasets

  Discover public and freely available Cloud Life Sciences datasets hosted on Cloud Storage and BigQuery.