Create a Genomics Delta Lake

Genomics data is usually stored in specialized flat-file formats such as VCF or BGEN.

The example below shows how to ingest a VCF into a genomics Delta Lake table using Glow in Python (R, Scala, and SQL are also supported).

You can use Delta tables for second-latency queries, performant range-joins (similar to the single-node bioinformatics tool bedtools intersect), aggregate analyses such as calculating summary statistics, machine learning or deep learning.


We recommend ingesting VCF files into Delta tables once volumes reach >1000 samples, >10 billion genotypes or >1 terabyte.

VCF to Delta Lake table notebook