szpiech
commented
10 years ago If you are interested in calculating EHH decay curves, you can specify the core marker using the --ehh flag. For instance, if your core marker is named rs100 in your file, then you can use --ehh rs100 to calculate the EHH decay around that marker; currently I don't have a batch submission feature for --ehh. If you are planning to perform a genome-wide scan with iHS or XPEHH, then each marker in the data is used, in turn, as a core marker.
You must have genetic data (phased genotypes) in order to do these calculations. However if you do not have a genetic map, you may use the physical map (chromosome positions) in place. You would format your file in exactly the same way, except that in the genetic map column you would put the physical map information. You must still also have the physical map information in the normal column, so in this case you would have two identical columns of physical map information.
I am a newcomer in positive selection on EHH. I have a question on it: how to determine the core marks? If we have some background on the considered genes, we can set the core marks. However, in most cases, when we scan positive selection along genome, we do not have such information for each gene. Is it right? If I only have position information for SNPs and have no genetic information, can I still use selscan to scan positive selection? How to arrange the map file? leave the genetic information to 0? Thanks.