A new tool, vcfsim, developed by Paimon Goulart, a stellar undergraduate researcher in my lab! vcfsim allows for the quick and easy simulation (via parameterized msprime simulations) of "all-sites" vcfs, with arbitrary ploidy and amounts of missing data.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
vcfsim: flexible simulation of all-sites VCFs with missing data
VCFs are the most widely used data format for encoding genetic variation. By design, standard VCFs do not include data from sites where all individuals are homozygous for the reference allele ("invari...
www.biorxiv.org
February 4, 2025 at 2:50 AM
A new tool, vcfsim, developed by Paimon Goulart, a stellar undergraduate researcher in my lab! vcfsim allows for the quick and easy simulation (via parameterized msprime simulations) of "all-sites" vcfs, with arbitrary ploidy and amounts of missing data.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
We are pleased to announce JBrowse v3.0.0! This is the latest semver bump to our JBrowse 2 product line
For this release, we created new features for phased and polyploid VCFs. The new phased mode in particular can reveal interesting patterns of inheritance in trio VCFs
jbrowse.org/jb2/blog/202...
For this release, we created new features for phased and polyploid VCFs. The new phased mode in particular can reveal interesting patterns of inheritance in trio VCFs
jbrowse.org/jb2/blog/202...
January 30, 2025 at 2:43 AM
We are pleased to announce JBrowse v3.0.0! This is the latest semver bump to our JBrowse 2 product line
For this release, we created new features for phased and polyploid VCFs. The new phased mode in particular can reveal interesting patterns of inheritance in trio VCFs
jbrowse.org/jb2/blog/202...
For this release, we created new features for phased and polyploid VCFs. The new phased mode in particular can reveal interesting patterns of inheritance in trio VCFs
jbrowse.org/jb2/blog/202...
I'm looking to hire a postdoc to work on the RepAdapt + MacroMar projects, analysing genomic data from >130 species of plants, animals, and fungi (VCFs are processed, ready to go). Lots of potential for creativity and collaboration!
yeamanlab.weebly.com/uploads/5/7/...
yeamanlab.weebly.com/uploads/5/7/...
September 8, 2026 at 7:04 PM
I'm looking to hire a postdoc to work on the RepAdapt + MacroMar projects, analysing genomic data from >130 species of plants, animals, and fungi (VCFs are processed, ready to go). Lots of potential for creativity and collaboration!
yeamanlab.weebly.com/uploads/5/7/...
yeamanlab.weebly.com/uploads/5/7/...
Are you interested in the genomic basis of repeated adaptation? The RepAdapt group now has >70 members working to re-run their whole genome shotgun datasets through a common SNP calling pipeline, sharing VCFs, and working together to analyse data. Please contact me if you'd like to contribute!
May 8, 2025 at 8:24 PM
Are you interested in the genomic basis of repeated adaptation? The RepAdapt group now has >70 members working to re-run their whole genome shotgun datasets through a common SNP calling pipeline, sharing VCFs, and working together to analyse data. Please contact me if you'd like to contribute!
vcfsim: flexible simulation of all-sites VCFs with missing data www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/Pie115/Vcfsi...
March 5, 2025 at 9:00 PM
vcfsim: flexible simulation of all-sites VCFs with missing data www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/Pie115/Vcfsi...
Behringer Releases Oberheim-Style Synth : 2-XM features 4 VCOs, 2 Multi-Mode VCFs, 2 LFOs and 4 Envelopes in Eurorack Format
2-XM features 4 VCOs, 2 Multi-Mode VCFs, 2 LFOs and 4 Envelopes in Eurorack Format
Behringer Releases Oberheim-Style Synth : 2-XM features 4 VCOs, 2 Multi-Mode VCFs, 2 LFOs and 4 Envelopes in Eurorack Format
sonicstate.com
April 4, 2025 at 1:15 AM
Behringer Releases Oberheim-Style Synth : 2-XM features 4 VCOs, 2 Multi-Mode VCFs, 2 LFOs and 4 Envelopes in Eurorack Format
Yeah I do my taxes in vcfs. I also wrote a blog post about why they’re bad for next gen sequencing data. It’s a short read.
June 19, 2025 at 2:53 AM
Yeah I do my taxes in vcfs. I also wrote a blog post about why they’re bad for next gen sequencing data. It’s a short read.
Using Rust
for Bioinformatics
tackling the complexity of VCF
with a common scripting language (lua)
Color me intrigued!
github.com/brentp/vcfex...
for Bioinformatics
tackling the complexity of VCF
with a common scripting language (lua)
Color me intrigued!
github.com/brentp/vcfex...
March 6, 2025 at 5:27 PM
Using Rust
for Bioinformatics
tackling the complexity of VCF
with a common scripting language (lua)
Color me intrigued!
github.com/brentp/vcfex...
for Bioinformatics
tackling the complexity of VCF
with a common scripting language (lua)
Color me intrigued!
github.com/brentp/vcfex...
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs. #VCF #VariantFiltering #RUST @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs
Motivation Variant Call Format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequencing experiments. Downstream analyses require the ab...
www.biorxiv.org
December 22, 2024 at 1:53 PM
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs. #VCF #VariantFiltering #RUST @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The VCF SoCal Learn to Solder Badge is back in-stock over at FVResearch - Thanks, Brian!
www.fvresearch.com/product/vcfs...
#LearnToSolder #ElectronicBadge #VCFSoCal #VCF #Festivals #VintageComputing #RetroComputers #RetroGaming #FUN
www.fvresearch.com/product/vcfs...
#LearnToSolder #ElectronicBadge #VCFSoCal #VCF #Festivals #VintageComputing #RetroComputers #RetroGaming #FUN
February 27, 2025 at 6:45 PM
The VCF SoCal Learn to Solder Badge is back in-stock over at FVResearch - Thanks, Brian!
www.fvresearch.com/product/vcfs...
#LearnToSolder #ElectronicBadge #VCFSoCal #VCF #Festivals #VintageComputing #RetroComputers #RetroGaming #FUN
www.fvresearch.com/product/vcfs...
#LearnToSolder #ElectronicBadge #VCFSoCal #VCF #Festivals #VintageComputing #RetroComputers #RetroGaming #FUN
🚀 Truvari v5.0 is here! 🎉
What’s new?
🔹 Enhanced symbolic variant support for, ,
🔹 Robust BND comparison for cross-representation SV matching
🔹 Improved SV sequence similarity & HUGE SV support
🔹 Cleaner UI & Revamped API
👉 More: github.com/ACEnglish/tr...
#Genomics #Bioinformatics
What’s new?
🔹 Enhanced symbolic variant support for
🔹 Robust BND comparison for cross-representation SV matching
🔹 Improved SV sequence similarity & HUGE SV support
🔹 Cleaner UI & Revamped API
👉 More: github.com/ACEnglish/tr...
#Genomics #Bioinformatics
GitHub - ACEnglish/truvari: Structural variant toolkit for VCFs
Structural variant toolkit for VCFs. Contribute to ACEnglish/truvari development by creating an account on GitHub.
github.com
January 10, 2025 at 1:43 PM
🚀 Truvari v5.0 is here! 🎉
What’s new?
🔹 Enhanced symbolic variant support for, ,
🔹 Robust BND comparison for cross-representation SV matching
🔹 Improved SV sequence similarity & HUGE SV support
🔹 Cleaner UI & Revamped API
👉 More: github.com/ACEnglish/tr...
#Genomics #Bioinformatics
What’s new?
🔹 Enhanced symbolic variant support for
🔹 Robust BND comparison for cross-representation SV matching
🔹 Improved SV sequence similarity & HUGE SV support
🔹 Cleaner UI & Revamped API
👉 More: github.com/ACEnglish/tr...
#Genomics #Bioinformatics
1/ You’ve got dozens of VCFs from a sequencing project.
But here’s the problem:
Which variants are shared across multiple samples? 🧵
But here’s the problem:
Which variants are shared across multiple samples? 🧵
August 21, 2026 at 1:45 PM
1/ You’ve got dozens of VCFs from a sequencing project.
But here’s the problem:
Which variants are shared across multiple samples? 🧵
But here’s the problem:
Which variants are shared across multiple samples? 🧵
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...
academic.oup.com/bioinformati...
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs
AbstractMotivation. Variant Call Format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequ
academic.oup.com
March 6, 2025 at 3:05 PM
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...
academic.oup.com/bioinformati...
1/ You’ve got dozens of VCFs from a sequencing project.
But here’s the problem:
Which variants are shared across multiple samples? 🧵
But here’s the problem:
Which variants are shared across multiple samples? 🧵
June 25, 2025 at 1:45 PM
1/ You’ve got dozens of VCFs from a sequencing project.
But here’s the problem:
Which variants are shared across multiple samples? 🧵
But here’s the problem:
Which variants are shared across multiple samples? 🧵
I see these videos of other VCFs and recognize that even though VCF West is located where a lot of the tech originated we don't have the square footage/basements where people can store huge collections
June 12, 2026 at 5:08 AM
I see these videos of other VCFs and recognize that even though VCF West is located where a lot of the tech originated we don't have the square footage/basements where people can store huge collections
vcfs vs ring mod w/ an all-analog sequence around the +ncom
simple - nothing finished, but the self-driving changes to the stereo field, timbre, and note articulation held my attention while making it on this rainy Seattle / Vashon day
#eurorack #sergemodular
youtu.be/wRcGpgG6bWA?...
simple - nothing finished, but the self-driving changes to the stereo field, timbre, and note articulation held my attention while making it on this rainy Seattle / Vashon day
#eurorack #sergemodular
youtu.be/wRcGpgG6bWA?...
Serge VCFS vs Ringmod
YouTube video by Navicore
youtu.be
December 23, 2024 at 1:32 AM
vcfs vs ring mod w/ an all-analog sequence around the +ncom
simple - nothing finished, but the self-driving changes to the stereo field, timbre, and note articulation held my attention while making it on this rainy Seattle / Vashon day
#eurorack #sergemodular
youtu.be/wRcGpgG6bWA?...
simple - nothing finished, but the self-driving changes to the stereo field, timbre, and note articulation held my attention while making it on this rainy Seattle / Vashon day
#eurorack #sergemodular
youtu.be/wRcGpgG6bWA?...
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs https://www.biorxiv.org/content/10.1101/2024.11.05.622129v1 🧬🖥️ 🦀 https://github.com/brentp/vcfexpress
November 6, 2024 at 9:00 PM
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs https://www.biorxiv.org/content/10.1101/2024.11.05.622129v1 🧬🖥️ 🦀 https://github.com/brentp/vcfexpress
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
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/examples at main · brentp/vcfexpress
expressions on VCFs. Contribute to brentp/vcfexpress development by creating an account on GitHub.
github.com
February 4, 2025 at 5:05 PM
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
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
In 2006 stond ik met mijn verhaal in de mijn geheim.
Ik was toen 24 en zat nog volop in t acceptatie proces van #22q11ds. Helaas is dit syndroom nog steeds onbekend en daar baal ik van.😟
Overigens heette het toen nog VCFs.
Ik was toen 24 en zat nog volop in t acceptatie proces van #22q11ds. Helaas is dit syndroom nog steeds onbekend en daar baal ik van.😟
Overigens heette het toen nog VCFs.
March 5, 2025 at 7:14 PM
In 2006 stond ik met mijn verhaal in de mijn geheim.
Ik was toen 24 en zat nog volop in t acceptatie proces van #22q11ds. Helaas is dit syndroom nog steeds onbekend en daar baal ik van.😟
Overigens heette het toen nog VCFs.
Ik was toen 24 en zat nog volop in t acceptatie proces van #22q11ds. Helaas is dit syndroom nog steeds onbekend en daar baal ik van.😟
Overigens heette het toen nog VCFs.
I've been to VCFs East and Montreal but Midwest is a bucket list for sure.
September 12, 2026 at 12:49 AM
I've been to VCFs East and Montreal but Midwest is a bucket list for sure.
1/ You’ve got dozens of VCFs from a sequencing project.
But here’s the problem:
Which variants are shared across multiple samples? 🧵
But here’s the problem:
Which variants are shared across multiple samples? 🧵
November 12, 2025 at 2:45 PM
1/ You’ve got dozens of VCFs from a sequencing project.
But here’s the problem:
Which variants are shared across multiple samples? 🧵
But here’s the problem:
Which variants are shared across multiple samples? 🧵
do I know any geneticists/molecular biologists/proteomics people who can help my friend Emma make sense(lol) of her VCFs (like I don't even think we're talking SINGLE nucleotide polymorphisms at this point)
August 6, 2025 at 12:18 AM
do I know any geneticists/molecular biologists/proteomics people who can help my friend Emma make sense(lol) of her VCFs (like I don't even think we're talking SINGLE nucleotide polymorphisms at this point)
AdaGenes: A streaming processor for high-throughput annotation and filtering of sequence variant data. #GeneticVariants #VariantFiltering #VariantAnnotation #VCFs #Genomics #Bioinformatics @biorxiv-bioinfo.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
June 28, 2025 at 6:06 PM
AdaGenes: A streaming processor for high-throughput annotation and filtering of sequence variant data. #GeneticVariants #VariantFiltering #VariantAnnotation #VCFs #Genomics #Bioinformatics @biorxiv-bioinfo.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Can you run sequential slurm arrays with one job submission? E.g., make bam files for all inds, then make individual VCFs when bam step is complete.
I currently do this with separate job submissions, but would like to combine into one job submission.
Thanks! #bioinformatics
I currently do this with separate job submissions, but would like to combine into one job submission.
Thanks! #bioinformatics
January 15, 2025 at 12:16 AM
Can you run sequential slurm arrays with one job submission? E.g., make bam files for all inds, then make individual VCFs when bam step is complete.
I currently do this with separate job submissions, but would like to combine into one job submission.
Thanks! #bioinformatics
I currently do this with separate job submissions, but would like to combine into one job submission.
Thanks! #bioinformatics