Best way of extracting individual VCFS from HAIL matrix

Hail Query & hailctl
1

I’m dealing with a HAL matrix made up of multiple individuals. I’m trying to think of the best (and least computationally-intensive) method and converting the matrix table into VCFs per each individual. One method I was thinking of was extracting IDs for each of the individuals, and creating some kind of loop to go over each sample, filter it down to just that individual, and then extract it out to a VCF.

If anybody has any better method, it would be much appreciative!

2

Hey @bioinformatics2024 ,

May I ask: why do you want to do this?

I have some experimental code to write a Hail Table for each column of a MatrixTable. You could give that a try.

You’d still need to serially convert each Hail Table to a VCF.