Hello team, I need to annotate each variants in a matrixtable with gene symbol and intervals for GRCh38. Is there a hail function to map genes with variants based on variant locus? Thanks very much for your help!

There is no such function. Your options: Download a GRCh38 locus to gene mapping file, import as a table, and use that to annotate your matrix table. Run hl.vep using a Dataproc cluster. Use the Hail Annotation Database to annotate gencode which has gene names. The Annotation Database is only avai…

@danking Thank you for the solution. I have used the option 3 you suggested to annotate the variants with genes using the gencode database. Some of the variants in my matrixtable are not mapped to any genes, since the locus of these variants are outside of any gene intervals. We would like to find …

There is no such function in Hail. If I was going to build that, I would take the ~30,000 genes and (just in Python or w/e) evenly expand their locus intervals until the entire genome is covered by at least one gene. Then I’d import that as a Hail table and use that to annotate my data.

@danking I am using the hail function below to load the gencode database on the DNAnexus platform. gencode = hl.experimental.load_dataset(name=‘gencode’, version=‘v31’, reference_genome=‘GRCh38’, region=‘us’, cloud=‘aws’) This function was running fine before last week. However, when I ran thi…

If you’re running Hail through DNANexus, this might be a bug in how they’re configuring Hail / Spark (especially if it was working last week). Looks like the culprit is a missing JAR for the AWS auth functionality.

Thanks @tpoterba for the quick reply. I am using the code below before the above function call. from pyspark.sql import SparkSession import hail as hl builder = ( SparkSession .builder .enableHiveSupport() ) spark = builder.getOrCreate() hl.init(sc=spark.sparkContext) I got the message be…

No, you need to contact DNANexus and ask them to fix this issue. They must’ve changed the Hail installation.

Annotate variants with genes

Hail Query & hailctl

shengwei66 May 22, 2023, 7:12pm 10

@danking Thanks for your quick reply. I will contact the DNANexus to fix this issue.

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Annotate variants with genes

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