With help from contributors, echtvar is still improving: github.com/brentp/echtvar

github.com/brentp/blamm... Does QC and EDA for long reads. It was written entirely by LLM.

New version of somalier is up: github.com/brentp/somal... Has a CHARR contamination estimator, a CONPAIR pair-wise inter-sample contaminatoin estimator, an AB/depth plotter and other improvements to make it of greater utility in cancer samples.

as part of my work with isabl genomics, I've been updating somalier with more info for cancer samples (contamination and concordance). somalier extracts small "sketches" of ~20K sites from a BAM/CRAM/VCF and then does rapid all-vs-all kinship checks. (1/n)

the codex desktop app was only available as a Mac DMG. A while ago, I downloaded it and told codex cli to make it work on linux. It did. Now I use that nearly exclusively. gist.github.com/brentp/b6bd8...

Again, I think making a custom GPT (or similar) as I did for bedder will be the default for most software shortly. If it can't answer common questions, improve the docs and refresh and the maintenance burden of answering user questions goes down.

Brent Pedersen, Mitchell Vollger and I have "posted" our preprint of the manuscript describing bedder, a complement to the functionality of bedtools. The "preprint server" we have chosen is google docs because it was rejected by biorxiv. docs.google.com/document/d/1...

I would guess that soon, every tool will have one of these. It is more interactive than just documentation and better than waiting for a grumpy maintainer to answer the same question in a github issue or personal email.

Feeding my markdown docs to this, then using it in anger shows where the docs need to be bolstered and provides a nice reference for users: help.openai.com/en/articles/... here's one for bedder: chatgpt.com/g/g-69a6027f...

I had a similar, less principled way of doing this, but this does seem to work quite well after trying a couple of large changes with it: boristane.com/blog/how-i-u... (I use codex, but same idea)

AGENTS.md > skills vercel.com/blog/agents-...

scratch that. better to use gemini-cli, turn on preview features and then get gemini 3.0 pro and flash for free for a decent amount each day.

crush coding agent with a free plan from cerebras using glm4.7 model is an easy way to start with coding cli tools. inference-docs.cerebras.ai/support/rate... github.com/charmbracele... crush is static binary that detects your CEREBRAS_API_KEY. GLM 4.7 isn't as good as Opus, but it is very solid.

another reminder about htsvcf which allows either 1. rust library to support javascript expressions (filtering/modification) on variants from VCF/BCF 2. javascript (node/bun) library for reading/writing/modifying variants from vcf/bcf. both very performant. github.com/brentp/htsvcf

a post about how, with LLMs, I wrote a new set of libraries. Wrapping htslib is my hello-world but doing it in rust to allow javascript expressions handled by V8 was more substantial project. The tools and LLMs are now getting quite good: brentp.github.io/latest/blog/... let me know what you think

my LLM-coded version of the single-page year calendar that's been going around. This one can be scripted with javascript to highlight cells, change the borders and texts. It also allows saving and sharing via url: brentp.github.io/single-page-... with code here: github.com/brentp/singl...

so Opus 4.5 is excellent for coding. I've been using these LLMs for coding for a while and it felt like slow improvement with each new model and sometimes more work to guide the model. Opus 4.5 just works. It solves hard problems and has good taste. Anyone else notice this?

I'll write more about this later, but as an experiment in LLM coding (GPT-5.2 and Opus 4.5), I wrote a JS wrapper for rust-htslib to read/write modify VCFs: www.npmjs.com/package/htsvcf works on linux (x64/aarch64) and OSX. brentp.github.io/htsvcf/lates...

Get bedder v0.1.8 and r𝗲𝗮𝗱 𝘁𝗵𝗲 𝗱𝗼𝗰𝘂𝗺𝗲𝗻𝘁𝗮𝘁𝗶𝗼𝗻 here: github.com/quinlan-lab/... We are looking for researchers to kick the tires, integrate bedder into their pipelines, and provide feedback on the Python functions, performance, and overall user experience! Please share and give us your feedback.

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

Aardvark? github.com/PacificBiosc...

I vaguely recall seeing #bioinformatics tool that could compare variants (or set of variants) using haplotypes rather than simply normalize and check for equality. That murky description is about as specific as I can get. Any pointers? IIRC, it's not just a truth-set evaluation tool. Has API

how do we feel about putting JSON in the INFO field of a VCF?

This is very cool work and I'm happy to see it published. Vcfexpress by @brent-p.bsky.social and @aaronquinlan.bsky.social allows building (essentially) arbitrary VCF filters expressed in lua code with parsing & eval powered by rust! academic.oup.com/bioinformati...

vcfexpress applies simple user expressions variants in a VCF. it can replace one-off python scripts to manipulate VCFs, likely with better performance. we'd like to collect use-cases here: github.com/brentp/vcfex... if you have a use-case and want some pointers, open an issue

vcfexpress is a command-line tool built in rust that lets users apply lua expressions to modify or filter a vcf from the command-line github.com/brentp/vcfex... new release with better docs github.com/brentp/vcfex... and examples github.com/brentp/vcfex...

I am looking for a mentor for the rust programming language. My latest issue is with trait bounds (github.com/brentp/simpl...) but I have a few things I generally hit. I can compensate with $$ or interesting problems. :) Please share with relevant people and feel free to DM.

with Jason K from @aaronquinlan.bsky.social lab, I have been dusting off fraguracy, which evaluates sequencing error rates using the portion of bases from paired end reads that overlap. New release adds, among other niceties, tracking for distance to homopolymers github.com/brentp/fragu...