Hello all! I have a dataset with quads (father, mother, proband, unaffected sibling). I am planning to use trio_matrix with all four members under the same family ID (proband’s ID). As I am interested in mtDNA, I am planning to filter out denovo variants that are homo/heteroplasmic in the child, but homozygous reference in the mother using proband_entry and mother_entry.
If I am using quad data with a Trio Matrix, can I check if this behavior makes sense? Thank you.
I think the trio_matrix abstraction won’t directly work here, but it’s certainly possible to do something like:
trio_mat = trio_mat.key_cols_by('fam_id')
trio_mat = trio_mat.collect_cols_by_key()
now you have the array of all trios per fam_id in the entry of the resulting matrix, and if you have a way to identify the proband from unaffected sib you can write the filter above.