Question regarding Inheritance genotype filter for trios

[tommyli]

Hi,

I'd like to ask about the expected behaviour when using the genotype inheritance filter. Our most recent merge with upstream (as of 2023-07-05, previous merge was 2023-01-16) resulted in some behaviour change in results. We noticed when only one sample has a genotype selected in a family of trio, then only that sample includes genotype information in the variant results. Is this expected behaviour? I noticed the genotype dropdown does not include the "any" option (i.e. 0, 1 and/or 2 alt alleles) but blank used to behave that way. I'd like to understand the use case(s) for this behaviour.

See below screenshots:

Sorry, I tried using taking screenshots from https://seqr.broadinstitute.org/ instead but I had trouble logging in (infinite OAuth redirects 🤷 ).

FYI, after some debugging, this is the line for this behaviour:

seqr/seqr/utils/search/utils.py

Line 356 in c200fdc

samples = _filter_genotype_samples(samples, inheritance_filter)

[hanars]

thanks for identifying this, it is a bug, all the available genotypes should be shown