All developed by @brent-p.bsky.social

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.

4. 𝗦𝗶𝗺𝗽𝗹𝗶𝗳𝗶𝗲𝗱 𝘀𝘆𝗻𝘁𝗮𝘅: We've streamlined the intersection logic, replacing complex flags like -wao, -f, and -r with clearer, modular options for defining intersection requirements.

3. 𝗨𝘀𝗲 𝗼𝗳 𝗶𝗻𝗱𝗶𝗰𝗲𝘀 𝗳𝗼𝗿 𝗵𝗶𝗴𝗵 𝗽𝗲𝗿𝗳𝗼𝗿𝗺𝗮𝗻𝗰𝗲 𝗼𝗻 𝗹𝗮𝗿𝗴𝗲 𝗱𝗮𝘁𝗮 𝘀𝗲𝘁𝘀: bedder is engineered to utilize file indexing (e.g., VCF indexes), resulting in dramatically faster queries, especially when intersecting against massive indexed datasets like gnomAD.

2. 𝗩𝗖𝗙 𝗜𝗻𝘁𝗲𝗴𝗿𝗮𝘁𝗶𝗼𝗻: For the first time, you can easily update VCF INFO fields based on interval overlaps, opening up new possibilities for variant annotation and processing.

Here is a high-level summary of what is innovative about #𝗯𝗲𝗱𝗱𝗲𝗿:
𝗖𝘂𝘀𝘁𝗼𝗺 𝗟𝗼𝗴𝗶𝗰 𝘄𝗶𝘁𝗵 𝗣𝘆𝘁𝗵𝗼𝗻: bedder has a flexible Python interface that allows you to define custom functions to process intersection fragments on the fly. This enables custom analyses without the need for endless command-line options.

Developed in Rust for speed and efficiency, bedder is designed to overcome the analytical limitations of traditional interval-based tools by putting analytical flexibility directly into your hands.

Please read our detailed 𝗯𝗹𝗼𝗴 𝗽𝗼𝘀𝘁: quinlanlab.org/blogposts/be...

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The symposium will feature rising science stars with research programs in evolutionary genetics and genomics, functional and disease genetics, and computational genomics. This is always a fun, rewarding, and exciting event!

We invite postdocs to apply and share their research among a broad group of scientists working in broad areas of genetics and genomics.

Thank you, Bruce!