Import VCF from GnomAD

Import VCF from GnomAD


Hi all, new to bioinformatics and have what I think is a pretty basic question. I’m attempting to use hail to import a vcf file from the gnomad website ( I’ve successfully created a python session in the terminal and loaded hail, now just trying to use import_vcf(), which should work by just taking one argument, the path to the file.

In [8]: chr1_test_file =

Here is my warning:

2019-09-20 15:24:25 Hail: WARN:
refers to no files

I imagine my problem is just that I don’t have the correct path, but I wasn’t quite sure what that would be…





Specifying a file path starting with / is relative to the root directory, and it probably isn’t want you want. A . refers to the current working directory, so there’s a good chance ./gnomad-public/... would work.

This is bioinformatics-adjacent as opposed to being a pure bioinformatics question, so you may have better luck with these questions on StackOverflow in the future.

before adding your answer.

Traffic: 2527 users visited in the last hour

Read more here: Source link