6 SNP Window Size

The window size of the SNP window used to pick the partner SNP for each anchor SNP is configurable using the -window-size option. It is only possible to set the SNP window size to an even number since the SNP window is in front and behind the anchor SNP. For example, to set the SNP window to size 12:

./snipsnip -window-size 12 -o myresults.dat mydata.bed

There is no “correct” window size, but 10 has proved in practise to be a good comprise between too small and too big, and is therfore set as the default. It is unlikely that a SNP window size of 20 or greater will be useful. If performing multiple GWASs with different SNP window sizes care should be exercised for multiple testing issues.

It is also possible to set the SNP window using base pair position, so that any SNP within a certain base pair position distance of the anchor SNP is considered for the partner SNP. For example, to set the SNP window a base pair position size of 110,000:

./snipsnip -window-size-bp 110000 -o myresults.dat mydata.bed

However, it is recommended to use a fixed number of SNPs for the SNP window to increase the chances of picking a good partner SNP.

Again, for more details concerning the methodology, please read the accompanying manuscript Howey and Cordell (2014).