Please move the updated ebuild form science overlay. It is true vcftools is superseded by bcftools but some people or tools still look for the vcftools package.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dc7beed7f021c6afe109a71cd67a3cf014538a57 commit dc7beed7f021c6afe109a71cd67a3cf014538a57 Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org> AuthorDate: 2022-02-19 14:05:07 +0000 Commit: Andrew Ammerlaan <andrewammerlaan@gentoo.org> CommitDate: 2022-02-19 14:05:12 +0000 sci-biology/vcftools: add version 0.1.16 Closes: https://bugs.gentoo.org/833503 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> sci-biology/vcftools/Manifest | 1 + sci-biology/vcftools/vcftools-0.1.16.ebuild | 37 +++++++++++++++++++++++++++++ 2 files changed, 38 insertions(+)