Weixuan Fu

You can simply use accuracy or f1 score on all of 20 samples that used in TPOT. It is noted that it is a training score instead of holdout/test score....

Sorry, I am not familiar with log loss so I am not sure whether it is logic for this case. It also depends on your study objectives. If f1 score...

Hi @brentp thank you for replying this issue so quickly. I made some mocked files to reproduce this issue. The 1st set is a trio (attached trio.zip) that mentioned above....

Correction for test 3 above. It works with `export SLIVAR_FORMAT_STRINGS=1`

I also tested duo family structure: [duo.nodad.zip](https://github.com/brentp/slivar/files/12359670/duo.nodad.zip) [duo.nomom.zip](https://github.com/brentp/slivar/files/12359671/duo.nomom.zip) Test 4. duo of kid + mom (kid (GT=1)+mom (GT=0/1) in duo.nodad.zip) with commend below, silver cannot pick the 2 variants ```...

I have made another duo with kid + mom but only change kid's GT from 1 to 1/1 in vcf (kid's GT = 1/1 and mom' GT = 0/1), then...

I checked the [source codes](https://github.com/brentp/slivar/blob/71a2bf2cc94746530a00a347564a8f04dd894ca9/src/slivarpkg/tsv.nim#L33-L45) about genotypes. the kid.alts should be -1 in this mix type GT in vcf. So if I change the function `proband_has_variant` from ``` function proband_has_variant(proband)...

will silvar have better support for hemizygous genotypes? like alts=4 for hem-ref and alts=5 for hem-alt.

Thank you! Could you please let me know how to compile the beta version of silvar from source codes? I need it to test the logic below: ``` (proband.alts >...

The PR #798 was just merged with a patch. If you want to try the dev branch, the command below can be used for installing dev branch to your environment:...