Identify inherited variants in trio matrix

Hail Query & hailctl
1

Hi,

I have a question regarding using the trio matrix to identify inherited variants?

I have already identified de novo variants, but do not find a function that could identify inherited variants. Besides, the property that variants are inherited from either one parent, I would also want to put a filter on the variants, such as GQ should be above 25, heterozygous genotypes with allele balance above 0.3.

Here’s the beginning of my code:
pedigree = hl.Pedigree.read(‘SSC.fam’)
mt_pass_QC_trio_dataset = hl.trio_matrix(mt_pass_QC, pedigree, complete_trios=True)

Any help would be appreciated.

Thank you.

2

What inheritance pattern are you looking for? I’d think that every heterozygous call in a proband is inherited, unless both parents are homozygous reference.

3

Thanks for your reply.

I think my question can be separated as:

  1. how to identify heterozygous variants.
  2. how to identify which heterozygous variants are from the proband.

Should I start from the trio matrix or the matrix table (mt_pass_QC in my example)? I saw the data structure is quite different in the trio matrix compared with the matrix table. But I thought trio matrix might be more accessible for variants in proband identification.

Thank you!

4

Starting from the trio matrix is going to be the right launching point for both, I think.

You can filter to entries that are heterozygous in the proband as follows:

tm = mt_pass_QC_trio_dataset # short name
tm_het = tm.filter_entries(tm.proband_entry.GT.is_het())