Combine non human gvcf with new_combiner reports errors

Hail Query & hailctl
1

i have thousends of rice gvcf, and i tryed to combine them with hail’s new_combiner function, but report errors.

ValueError: Unsupported reference genome 'IRGSP_1_0', only 'GRCh37' and 'GRCh38' are supported

can new_combine surpport non human genome?

here is my test code.

import hail as hl

hl.init()

irgsp_ref = hl.ReferenceGenome.from_fasta_file(
    name='IRGSP_1_0',
    fasta_file="IRGSP-1.0_genome.fasta",
    index_file="IRGSP-1.0_genome.fasta.fai",
)

gvcfs = [
    '/home/hail/01_each/sample0001.gatk.g.vcf.gz',
    '/home/hail/01_each/sample0002.gatk.g.vcf.gz',
    '/home/hail/01_each/sample0003.gatk.g.vcf.gz',
    '/home/hail/01_each/sample0004.gatk.g.vcf.gz',
]

combiner = hl.vds.new_combiner(
    output_path='/home/hail/tmp/dataset.vds',
    temp_path='/home/hail/tmp/tmp/',
    gvcf_paths=gvcfs,
    use_genome_default_intervals=True,
    reference_genome=irgsp_ref,
)

combiner.run()

vds = hl.read_vds('/home/hail/tmp/ataset.vds')
2

You can’t use use_genome_default_intervals=True. You’ll need to specify intervals manually. Our method of calculating default intervals ignores alternate contigs, and we don’t know what contigs are alternate in user provided reference genome.