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List-Annotation.md

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Section 2: List Available Public Annotation Datasets

This part of the code demonstrates how to list AnnotationHive's public datasets.

  • To list all available annotation datasets, run the following command:

    mvn compile exec:java -Dexec.mainClass=com.google.cloud.genomics.cba.StartAnnotationHiveEngine -Dexec.args="BigQueryAnnotationRepository --project=<YOUR_Google_Cloud_Project_ID> --bigQueryDatasetId=<Google_Cloud_Project_ID>:<BigQuery_Dataset_ID> --runner=DataflowRunner" -Pdataflow-runner

    Note: The bigQueryDatasetId for this command requires to have the full address including the project ID.

  • To list only annotation datasets with the same build, set annotationDatasetBuild. Here is an example for hg19:

    mvn compile exec:java -Dexec.mainClass=com.google.cloud.genomics.cba.StartAnnotationHiveEngine -Dexec.args="BigQueryAnnotationRepository --project=<YOUR_Google_Cloud_Project_ID> --bigQueryDatasetId=<Google_Cloud_Project_ID>:<BigQuery_Dataset_ID> --annotationDatasetBuild=hg19 --runner=DataflowRunner" -Pdataflow-runner

  • To find and list all annotation datasets that have a particular keyword, set --searchKeyword. Here is an example for the keyword sample:

    mvn compile exec:java -Dexec.mainClass=com.google.cloud.genomics.cba.StartAnnotationHiveEngine -Dexec.args="BigQueryAnnotationRepository --project=<YOUR_Google_Cloud_Project_ID> --bigQueryDatasetId=<Google_Cloud_Project_ID>:<BigQuery_Dataset_ID> --searchKeyword=sample --runner=DataflowRunner" -Pdataflow-runner

  • To find and list all annotation datasets of the same type (i.e., generic or variant), set --annotationType. Here is an example for generic:

    mvn compile exec:java -Dexec.mainClass=com.google.cloud.genomics.cba.StartAnnotationHiveEngine -Dexec.args="BigQueryAnnotationRepository --project=<YOUR_Google_Cloud_Project_ID> --bigQueryDatasetId=<Google_Cloud_Project_ID>:<BigQuery_Dataset_ID> --annotationType=generic --runner=DataflowRunner" -Pdataflow-runner

  • You can also run any combination of the abovementioned cases. Here is an example for how to find all annotation datasets that are hg19, contain the keyword sample, and they are the variant type:

    mvn compile exec:java -Dexec.mainClass=com.google.cloud.genomics.cba.StartAnnotationHiveEngine -Dexec.args="BigQueryAnnotationRepository --project=<YOUR_Google_Cloud_Project_ID> --bigQueryDatasetId=<Google_Cloud_Project_ID>:<BigQuery_Dataset_ID> --searchKeyword=Sample --annotationType=variant --annotationDatasetBuild=hg19 --runner=DataflowRunner" -Pdataflow-runner