How to setup my own non-human reference genome in hail?

Hail Query & hailctl
1

Hi all,
I would like analyze huge non-human vcf files and build my own non-human reference genome (ReferenceGenome object), but I can not find a way to set it up in hail 0.2. It looks like no way to me to set it via hail.init() or any other method like set_reference() in somewhere. Could you please help? Thanks in advance!

2

This is one of the rougher edges of Hail. It’s possible to set the default reference genome to one of the built-in ones (GRCh37, GRCh38, GRCm38, CanFam3) in hl.init, but most methods that import genetic data (import_vcf, import_bed, …) or create locus objects (hl.locus, hl.parse_locus, hl.parse_locus_interval, …) take a reference_genome argument. See the import_vcf docs for one example.

So you can do something like:

hl.init() # use default ref genome
your_reference_genome = hl.ReferenceGenome(...)
mt = hl.import_vcf(..., reference_genome=your_reference_genome)
mt.write('...')

Once you have a MatrixTable or Table that has a Locus key parameterized by your reference genome, you don’t need to continue defining it with hl.ReferenceGenome in every Hail session, it will be loaded every time you do hl.read_matrix_table on the written matrix table. If you need to grab it again, you can do so with mt.locus.dtype.reference_genome.

3

Hi Tim,
Thank you very much for the qiuck reply! It looks more intuitive that one can set it up in init method using ReferenceGenome rather than other place.

4

Yeah, agreed. This is non-trivial to implement because it’s a chicken-and-egg problem – we want to initialize Hail with a new reference genome but we need functionality from an initialized Hail session in order to create the new reference genome in the first place :disappointed: