Yale Peabody Museum Trip

On Monday, I headed up to the Yale Peabody Museum with Dr. Andy Burrell to sample some (non-primate) museum skins.

It was hard to work with these guys peeking over our shoulders:

But the taxidermied aardvark seemed glad to see us:

As did the happy aye aye:

Thanks a ton to the folks at Yale that made this sampling trip so easy and enjoyable! No wonder your taxidermy is so happy.

Concatenate VCF SNPs into a FASTA Alignment

A while back I published a script, vcf-tab-to-fasta, to make a FASTA alignment from VCF tab files (output from VCFtoolsvcf-to-tab utility). It just concatenates the SNPs, but it’s useful as a quick sanity check when working with massive SNP datasets since you can then easily bang out a neighbor joining tree or compute pairwise distances, etc. I thought I’d be the only one to use it, but I was happy to have it available in an open source repository regardless.

I was heartened to discover that people have actually been downloading and using it, with over 100 downloads not counting those that checked it out via SVN. A user was nice enough to point out a bug—the script won’t work on haploid SNPs, such as those found on the Y chromosome or in the mitochondrial genome. Whoop! I had only ever used it on autosomal DNA. The bug is now fixed and I’ve written up a quick tutorial for its use. Check it out here, and let me know if you ever find it handy!