Read VCF files using latest runtime version

[nachog99]

Hello everyone!

I was reading VCF files using the glow library (Maven: io.projectglow:glow-spark3_2.12:1.2.1).

The last version of this library only works with the spark's version 3.3.2 so if I need to use a newer runtime with a more recent spark version I receive an error because they aren't compatible.

How can I fix that? Does anyone know a different way to read VCF files? Or should I stick to a specific spark version to use this library

If someone have an idea I will appreciate it 

[Kaniz_Fatma]

Hi @nachog99, Working with VCF (Variant Call Format) files in Spark can be done using various approaches. Let’s explore some options:

1. Glow Library:

   • You’ve already been using the Glow library (Maven: io.projectglow:glow-spark3_2.12:1.2.1) to read VCF files. However, as you mentioned, it’s tied to Spark version 3.3.2.
   • If you want to use a newer Spark runtime with a more recent Spark version, you’ll need to address the compatibility issue.
   • One way to proceed is to check if there are any updated versions of the Glow library that support the Spark version you’re interested in. Keep an eye on their official documentation or community discussions for any announcements regarding...¹.

2. Native Spark VCF Reader:

   • Spark itself provides a native way to read VCF files using the DataFrame API.

   • You can use the following code snippet to read VCF files directly:

     vcf_path = "/path/to/your/vcf/file.vcf.gz"
     df = spark.read.format("vcf").load(vcf_path)
     

   • Replace "/path/to/your/vcf/file.vcf.gz" with the actual path to your VCF file.

   • This approach doesn’t require any additional libraries and should work with different Spark versions².