PSA, since I've now seen problems arising from this: As of Sept 2023, GATK no longer makes missing genotypes explicit in VCFs (i.e. './.' as in the VCF spec). Missing genotypes are instead coded as '0/0' with a DP=0 format field. See attached for examples.

As I manually edit ~50 LaTeX references to follow a journal's requirements, I wonder: why is the publishing process is so time consuming and frustrating?

It's because there isn't real competition. Journals are a non-collusive oligopoly. Things suck because of market conditions.

💀➡️🐒🧬
In this preprint, we show that we can accurately call IBD segments in over 100 imputed Macaque low-coverage genomes and then explore this precise signal of relatedness in a large pedigree.
A truly enjoyable collaboration with a great interdisciplinary team!

Taking identity-by-descent (IBD) analysis into the wild! biorxiv.org/content/10.110…
In this preprint, we leverage novel genomic methods to estimate fine-scale gradients of relatedness in animals and highlight their many applications in the field of ecology and evolution.🐒🧬 [1/3]

doi.org/10.1038/s41588… ancIBD is published now! 🧬💀

Our tool brings accurate IBD detection to aDNA. We show that this unlocks the detection of up to sixth-degree relatives in aDNA, and reveals new links between ancient cultures. A short summary ⬇️ (1/5)

Most folks in computational genetics/genomics are well aware of the log-sum-exp trick to avoid numerical over/under flow.
But I thought it might be helpful to highlight some useful functions to improve the numerics of other common operations. 1/n

The age of IBD in ancient DNA is nigh! doi.org/10.1101/2023.0…
In this preprint, we describe 'ancIBD', a method to detect long shared haplotypes (known as IBD segments) in human ancient DNA data, and showcase applications. 🧬💀 (1/5)

We released a commentary on Ioannidis et al (2021) as a preprint. To date the settling of Polynesian islands, they inferred split times using IBD segments shared between modern genomes. We show that their estimator is biased to be ca. 300 years too old. doi.org/10.1101/2022.1…