Brent Pedersen

`proband_has_variant` is not in the js that I distribute with slivar, so you'll have to share that code.

slivar is most tested on diploid variants but I think this should work. Are you using the latest version?

please try with latest then we will check from there.

can you try with latest version? if the results are not what you expect, then send a valid VCF with the 2 variants and the VCF header and I will...

ok. I think that's a better way to go. alts really makes most sense for diploid variants. also, I think you shouldn't use both --ped and --alias

Yes, I committed last month code to handle accessing the genotype: https://github.com/brentp/slivar/commit/9f7d995686f1324a9b94381c4ee2caf0feca501d so you'll be able to do `sample.GT` which would be `[0, 1]` for a heterozygous allele, and `[1]`...

You can try it the attached [slivar_dev.gz](https://github.com/brentp/slivar/files/12366846/slivar_dev.gz) just download, gunzip, chmod +x and run as ./slivar_dev

Hi Aaron, the only way to do this is with `--permissive-overlap` as you note. I think that's the correct behavior as "G ." should not match with G A". if...

mosdepth uses such a check (if read is strictly less than mate) and if not, it saves the read into a hashtable. I think that can work here, but I'm...

Hi sorry for the delay. I think using the DHFFC is the best filter, along with genotype.