Friday, July 1, 2011

Gists

I've been super busy writing a paper lately, so I apologize for the lack of updates. I do intend to comment on the recent 23andMe paper soon™.

A new feature on the blog is my Gist feed and a link to my Gist page. Gist is basically a quick-and-dirty code-sharing site from Github. Since I'm a quick-and-dirty bioinformatics programmer, I'll do my best to keep random code snippets that might have general application for others up there and publicly available. Also, please feel free to fork my code, fix it, et cetera.

My first Gist is an interesting one: A shell script for calculating mean heterozygous allele balance from a VCF4 file (basically GATK output with the "AB" INFO field). Very simplistic, but fast and easy to use for people wondering what the overall reference bias is in their variant calls.