Updates

12/11/18: BetaScan version 2 is released! This version has two main improvements: it implements a new Beta statistic which uses substitutions, and it can now standardize each Beta statistic by its variance. These updates are detailed in our bioRxiv preprint.

10/15/18: You can now specify the output file name using the -o flag. Both the -i and -o flag can take in gzipped files (see examples in "Sample Commands"). I'm also happy to announce that BetaScan format can now be generated from several file formats, including plink and vcf, by the toolkit glactools. Thank you to Gabriel Renaud for these updates!

7/5/17: Added some more checks for valid parameter choice and input file format. Also, slightly modified behavior of script when determining SNPs in the current window, so that core SNP is excluded from window size when the window size is even. This means that the window will now be symmetric around the core SNP, whether an odd or even window size parameter is given. Also, made a tweak so that performance should be slightly quicker than the older version.

5/4/17: Beta now can take in variable sample sizes for each SNP. In other words, not all frequencies have to be calculated using the same number of individuals. Because of this, the input file format has been updated.