Method for inherited variants?

Hail Query & hailctl
1

Hello. Can I know if there is an in-built method to call inherited variants from trios? I am interested in these scenarios:

  1. Het in one parent / het in child.
  2. Het in one parent / hom ref in child
  3. Het in both parents / hom alt in child
2

@pixel_123, you can use trio_matrix with a pedigree file to get a Matrix Table with an easy-to-use structure. From there your queries are relatively straightforward:

mt = mt.entries()
calls = mt.filter(
    (mt.proband_entry.is_het() & mt.father_entry.is_het() & ~mt.mother_entry.is_het())
    | (mt.proband_entry.is_het() & ~mt.father_entry.is_het() & mt.mother_entry.is_het())
)