Brent Pedersen

Hi @edg1983 , vcfanno doesn't support BCF. I should add a better message for that, but it will resolve your issue for now.

hmm. let me think about that. I think vep cache is just chunks of tabix indexed stuff, no? this would be a longer term (like 2026) project but it's possible.

Hi, smoove square is simply calling bcftools merge. That command suffers with large sample sizes such as yours. You might need to write your own (simply concat the columns).

I'm not sure why the logs wouldn't complete. But you should get a warning if the file is incomplete. And if it has an index then it must be fine.

thanks! does this fix the issue for you?

Hi, I'm happy to accept PRs that improve error messages.

hi, this should return reads in the correct bins, you also need to check the start and stop of each read to make sure it overlaps your region. I probably...

hi, there are no plans for this. All of the code assumes all-vs-all. I see the benefit of 1 vs all, and would accept a PR for it but I...

looks like it worked but you might look into why you have that odd field in the header.