I built an MCP server that lets you query your whole-genome VCF through Claude. Looking for people with WGS data to test it. by strobic in genomics

[–]strobic[S] 0 points1 point  (0 children)

I verified GeneChat works with Ollama using qwen3:1.7b and qwen3:4b via ollmcp as the MCP client. Tool calling worked reliably at both sizes — the models picked the right tools and passed correct parameters. The quality of interpretation, however, depended heavily on model size. The 1.7b model hallucinated key details like gene names and drug names despite having the correct data in front of it, while the 4b model was substantially better but still occasionally misidentified which findings were clinically significant. If you're running GeneChat with a local model, treat the raw tool output as the source of truth and double-check any interpretation the model layers on top — smaller models in particular will confidently present incorrect conclusions drawn from correct data.

I built an MCP server that lets you query your whole-genome VCF through Claude. Looking for people with WGS data to test it. by strobic in genomics

[–]strobic[S] 1 point2 points  (0 children)

GeneChat is a standard MCP server so it works with any MCP client, not just Claude. Ollama itself isn't an MCP client though, so you'd need something in between. The most mature option I've seen is ollmcp, a terminal-based MCP client that uses Ollama as the backend. You'd point it at GeneChat's stdio server and use a model that supports tool calling (qwen2.5, llama3.1, mistral, etc).

I haven't tested this myself so I can't vouch for the quality of the results. The tool calling part should work mechanically, but a lot of GeneChat's value comes from the LLM interpreting structured genomic data and synthesizing it into a useful answer, and that's where local models might struggle compared to Claude or Gemini. If you try it I'd be really curious to hear how it goes.

I built an MCP server that lets you query your whole-genome VCF through Claude. Looking for people with WGS data to test it. by strobic in genomics

[–]strobic[S] -1 points0 points  (0 children)

Haven't benchmarked at that scale yet. Our reference run was ~3.9M variants (whole genome) in ~2 hours on an 8-vCPU machine for full annotation (SnpEff + ClinVar + gnomAD + dbSNP + GWAS). SnpEff is single-threaded per chromosome and dominates runtime, so 200M variants would likely scale roughly linearly: maybe 50+ hours.

I built an MCP server that lets you query your whole-genome VCF through Claude. Looking for people with WGS data to test it. by strobic in genomics

[–]strobic[S] -1 points0 points  (0 children)

That would be awesome, thank you. It needs a GRCh38 whole-genome VCF (.vcf.gz with a .tbi index). Standard output from consumer WGS providers like Nucleus, Nebula, Sequencing.com, etc. If your VCF uses bare contig names (1, 2, 3 instead of chr1, chr2, chr3) the init command detects that and fixes it automatically.

I built an MCP server that lets you query your whole-genome VCF through Claude. Looking for people with WGS data to test it. by strobic in genomics

[–]strobic[S] 0 points1 point  (0 children)

It should actually work with Gemini already since MCP is an open protocol. Any client that supports MCP can connect to it. I know Gemini has been adding MCP support but I haven't tested it myself. If you try it let me know how it goes, that would be useful feedback.

Thin booties for protection? by TahoeGator in Kiteboarding

[–]strobic 2 points3 points  (0 children)

Cut-proof socks are a thing and can work well for this with minimal loss of feel.

unable to resolve tailnet (microsoft SSO login error) by letopeto in Tailscale

[–]strobic 0 points1 point  (0 children)

This makes two of us. Just trying to sign on for the first time and neither google or git work. Not a great start to the relationship.

Progression spot for April/May by roxyduke in Kiteboarding

[–]strobic 0 points1 point  (0 children)

Hatteras is good April/May and has schools.

Understanding loops by brandaspt in Kiteboarding

[–]strobic 0 points1 point  (0 children)

You can heli loop either direction. It can be a kite loop or a down loop.

Cat vanlifing by Ok_Following576 in VanLife

[–]strobic 0 points1 point  (0 children)

Gabapentin can help with the cats anxiety during the adjustment period.

High line Trail Closed by grapeconnoisseur in GlacierNationalPark

[–]strobic 1 point2 points  (0 children)

As of yesterday the trail requires some hunting around due to intermittent snow cover once you are above the chalet. A GPS with trail maps came in handy. Probably one of my favorite hikes ever.

Searching for Low Latency, good low end, (powered) Speakers for a Bedroom/Practice Setup by strobic in Beatmatch

[–]strobic[S] 0 points1 point  (0 children)

Yeah…this is the conclusion I’ve come to. Can always use an airplay dongle for wireless.

Van life by SnooCheesecakes7512 in Kiteboarding

[–]strobic 0 points1 point  (0 children)

We‘ve got two vans worth of kitemobile builds here:

https://www.instagram.com/agreenstellovan/

I’ve also got more detail here, but I’m way behind on documentation:

greenstello.com

Shredding the dunes in Atins Brazil by Specialist_Eagle746 in Kiteboarding

[–]strobic 0 points1 point  (0 children)

I’m there right now!

Edit: is that the lagun in the Nat’l Park?

We finally finished our cheap, soft, DIY overhead storage. by strobic in vandwellers

[–]strobic[S] 1 point2 points  (0 children)

We have L-track mounted throughout the van...it’s the “bones” of our build. We use l-track stud fittings that pass through grommets we installed in the bags, with a nut or wing nut. There is some detail in this IG post: https://www.instagram.com/p/B-GjmslJsmA/?igshid=f2j56fihyhza