#vep — Public Fediverse posts on home.social

SMT @[email protected] · 2026-07-21 · 20:51 UTC

The duckvep port of ensembl-vep consequence state machine for independent events (no haplosaurus for now) is shaping well, but still too slow single core ( ~ 250K variants per second on the genome). For real vep concordance we choosed to get ensembl mysql relations directly into a duckb relation tables as cache format. For supplementary annotations duckb native joins or cgranges are more than enough, no special formats, parquet/duckb tables are enough

#Bioinformatics #VEP

#bioinformatics #vep

SMT @[email protected] · 2026-06-14 · 13:14 UTC

Since i have some Slope Code credits, i say why not make a vibeslop duckvep version of (vibesloped) #fastVEP, sad to noticed that the headline concordances where implicitly hiding very consequential divergences from ensembl-vep's accumulated knowledge/art ! Other progress notes on this project will follow

#Bioinformatics #VEP

#fastvep #bioinformatics #vep

SMT @[email protected] · 2026-05-27 · 17:20 UTC

#Bioinformatics #VEP #DuckDB
I just got the realization that instead of trying to parse in C ensembl VEP's caches (ridiculous idea given the perl serialization format), duckdb has a mysql reader and i can just load this into duckdb the ensembl DB tables i need ! this make the duckvep project much more manageable and mostly sql kernel work now since we already have variant keys and cgranges udfs in the duckhts extension https://github.com/RGenomicsETL/duckhts

#bioinformatics #vep #duckdb

Auch_in_Bremen @[email protected] · 2025-06-21 · 03:36 UTC

@CyclePeda @lkwtelefon @fedibikes_de @Rad @tluhh das #asv hat kein wirkliches Interesse an #Fußgängern und #Radfahrern. Planungen für diese Bereiche werden (wenn überhaupt) schleppend gemacht und noch langsamer umgesetzt. Schöne Beispiele sind die #Brücken, oder überhaupt das Netz an #Premiumrouten aus dem #VEP. Die Anbindung der D15 nach Achim uvm.
Und Wegeführungen bei Baustellen sind wunderbar als Blockade geeignet.

#asv #fußgangern #radfahrern #brucken #premiumrouten #vep

SMT @[email protected] · 2025-05-03 · 19:47 UTC

academic.oup.com/bib/article/... #PathogenicityPrediction #xgboost #VEP #Bioinformatics

DS-MVP: identifying disease-sp...

#pathogenicityprediction #xgboost #vep #bioinformatics

RTE News Headlines @[email protected] · 2025-04-23 · 15:34 UTC

[17:22] RTÉ opens Voluntary Exit Programme with cap of €300,000

RTÉ has opened its Voluntary Exit Programme (VEP), as the broadcaster seeks to reduce staff numbers by up to 400.

https://www.rte.ie/news/business/2025/0423/1509112-rte-opens-voluntary-exit-programme-with-cap-of-300-000/

#RTÉ #VoluntaryExitProgramme #VEP #upto400

#rte #voluntaryexitprogramme #vep #upto400

MultiQC @[email protected] · 2025-04-09 · 08:15 UTC

Modules #QUAST and #Trimmomatic got minor updates, and #VEP and #BclConvert got bugfixes. There were also a number of tweaks and fixes for AI summaries ✨

See the full changelog here: https://github.com/MultiQC/MultiQC/releases/tag/v1.28

#quast #trimmomatic #vep #bclconvert