Pop_frequency_prior format in hail.methods.de_novo

Hail Query & hailctl
1

I’m trying to call de novo events using hail.methods.de_novo. In the example below (copied from the hail website), I’m wondering about the format for the gnomadFreq.tsv file specified on the second line. What should this file look like? Thanks so much.

>>> pedigree = hl.Pedigree.read('data/trios.fam')
>>> priors = hl.import_table('data/gnomadFreq.tsv', impute=True)
>>> priors = priors.transmute(**hl.parse_variant(priors.Variant)).key_by('locus', 'alleles')
>>> de_novo_results = hl.de_novo(dataset, pedigree, pop_frequency_prior=priors[dataset.row_key].AF)
2

This example would work on a file that looks like:

Variant    AF
1:1:A:T    0.2123
1:20:T:TT  0.0010
3

Thank you! Is the file used in the example available (or something similar?).

Could I annotate the rows of the matrix table with the population alternate allele frequency priors and use that for the pop_frequency_prior parameter?

4

Thank you! Is the file used in the example available (or something similar?).

That’s just an example. The gnomad data is available, though: gnomad.broadinstitute.org

Could I annotate the rows of the matrix table with the population alternate allele frequency priors and use that for the pop_frequency_prior parameter?

Yes, this is the intended use!

5

Thanks!