Readers will enjoy the following slides from Erik Garrison’s talk at Biology of Genome conference. He is trying to get video of his talk, and when it comes, we will link to the video as well.
Erik is doing his excellent work as a researcher (staff
scientist) at Gabor Marth’s lab at Boston College. You can access freebayes and other codes from his github page here. Gabor Marth is well known for his early work on SNP discovery in the last century and Erik’s ‘freebayes’ is name likely came from ‘polybayes’ algorithm mentioned in the following paper.
A general approach to single-nucleotide polymorphism discovery. Gabor T. Marth, Mark D. Yandell, Ian Korf, Zhijie Gu, Raymond T. Yeh, Hamideh Zakeri, Nathan O. Stitziel, LaDeana Hillier, Pui-Yan Kwok and Warren Gish. Nature Genetics 23, 452-456 (1999).
Unfortunately, the Nature Genetics paper itself is not free after 14 $%#$%# years!! These slides may be helpful, if you are interested in learning the algorithm. We will check to see whether Erik has plan to write a ‘freepaper’ algorithm to let others see Marth’s original manuscript :)
P. S. Erik responded with sending a link to his freebayes paper, thankfully deposited at arxiv.