Skip to content

Latest commit

 

History

History
41 lines (28 loc) · 5.71 KB

Gene-Annotation.md

File metadata and controls

41 lines (28 loc) · 5.71 KB
Raw

Section 6: Gene-based Annotation

This section demonstrates how to run our gene-based annotation process for a VCF/mVCF table.

There are two functionalities supported by AnnotationHive regarding gene annotation: 1) finding the closest gene to each variant, and 2) finding all genes that overlap with each variant within an input proximity threshold.

  • Finding the closest gene for each variant Here are the key options:

    • --geneBasedAnnotation=true
    • --geneBasedMinAnnotation=true
    mvn compile exec:java -Dexec.mainClass=com.google.cloud.genomics.cba.StartAnnotationHiveEngine -Dexec.args="BigQueryAnnotateVariants --projectId=<Your_Google_Cloud_Project_Name> --runner=DataflowRunner --stagingLocation=gs://<Your_Google_Cloud_Bucket_Name>/<Staging_Address>/ --bigQueryDatasetId=<YOUR_BigQuery_Dataset_ID> --genericAnnotationTables=<Table address Plus selected fields> (e.g., myProject:myPublicAnnotationSets.hg19_refGene:name:name2 - selecting name and name2 from hg19_refGene table) --VCFTables=<VCF_Table_Names>(e.g., genomics-public-data:1000_genomes_phase_3.variants_20150220_release) --outputBigQueryTable=<Output_Table_Name> --geneBasedAnnotation=true --geneBasedMinAnnotation=true --searchRegion=<chromID1:Start1:End1,Chrom2,Start2;...;ChromN:StartN:EndN>" -Pdataflow-runner

    Here is an example:

    mvn compile exec:java -Dexec.mainClass=com.google.cloud.genomics.cba.StartAnnotationHiveEngine -Dexec.args="BigQueryAnnotateVariants --projectId=<Your_Google_Cloud_Project_Name> --runner=DataflowRunner --stagingLocation=gs://<Your_Google_Cloud_Bucket_Name>/statging/ --bigQueryDatasetId=test --genericAnnotationTables=<Your_Google_Cloud_Project_Name>:AnnotationHive.hg19_UCSC_refGene:name:name2 --geneBasedAnnotation=true --geneBasedMinAnnotation=true  --outputBigQueryTable=BRCA1_BRAC2_closest_genes_test_chr17 --VCFTables=<Your_Google_Cloud_Project_Name>:test.NA12877_chr17 --searchRegions=chr17:41196311:41277499" -Pdataflow-runner

  • Finding all overlapped genes within a specific proximity threshold for each variant. Here are the key options:

    • --geneBasedAnnotation=true
    • --proximityThreshold=10000
    mvn compile exec:java -Dexec.mainClass=com.google.cloud.genomics.cba.StartAnnotationHiveEngine -Dexec.args="BigQueryAnnotateVariants --projectId=<Your_Google_Cloud_Project_Name> --runner=DataflowRunner --stagingLocation=gs://<Your_Google_Cloud_Bucket_Name>/<Staging_Address>/ --bigQueryDatasetId=<YOUR_BigQuery_Dataset_ID> --genericAnnotationTables=<Table address Plus selected fields> (e.g., myProject:myPublicAnnotationSets.hg19_refGene:name:name2 - selecting name and name2 from hg19_refGene table) --VCFTables=<VCF_Table_Names>(e.g., genomics-public-data:1000_genomes_phase_3.variants_20150220_release) --outputBigQueryTable=<Output_Table_Name> --geneBasedAnnotation=true --proximityThreshold=<An_Ineteger_Number>" -Pdataflow-runner