brent pedersen
@brent_p
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computational biologist. Building humane tools for large-scale genomics and rare-disease. Contact me if you have genomics/bioinformatics contracting work.
Corvallis, Oregon, USA
Joined October 2008
new release of vcfexpress with some performance improvements for common uses: also adding to list of examples, for example filtering on posterior genotype prob:
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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: if you have a use-case and want some pointers, open an issue
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already got a PR accepted to fix this. and then additional help to update my code. 👍
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RT @jiayi_pirate: We reproduced DeepSeek R1-Zero in the CountDown game, and it just works Through RL, the 3B base LM develops self-verifi…
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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 new release with better docs and examples
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@curious_coding @AndresGuarahino I got some help that I need to try out. stay tuned for further episodes of me crowd-sourcing rust problems
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with @JKunisaki from @aaronquinlan lab, 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 homopolymer.
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@ebioman @johanneskoester @aaronquinlan if you open an issue about what you'd like to do, it's possible we can implement or facilitate. there's a lot of control in the lua code even.
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@johanneskoester @aaronquinlan good idea. it's here: will add it to the paper before publication.
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echtvar still (echt waar) annotates variants extremely rapidly with large population databases where most variants are encoded into 32 bits (and are then compressed with stream v-byte). latest release fixes a small bug
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@johanneskoester @aaronquinlan it does not support BNDs. yes, similar in spirit to vembrane. note that we use the vembrane benchmark which was very nice to have. 👍
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RT @nomad421: Rust execution engine + Lua expressions, God what a great combination! This looks awesome. Congrats @brent_p and @aaronquinla…
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