When using the -f2 input format, why does PHASE use the wrong character for the minor allele?
With the -f2 input format, when there are no minor allele homozygotes at a site, PHASE has no way of knowing what the minor allele is. So it adopts the convention of using the character following the major allele alphabetically for the minor allele. For example, if the major allele is A then in its output PHASE uses B to represent the minor allele. Similarly, if the major allele is G then PHASE uses H for the minor allele. Q: I can’t unzip the PHASE.gz file. Why not? Some browsers seem to unzip this file automatically. Try renaming the file to be PHASE, setting it to be executable (eg chmod a+x PHASE), and running it. Q: I’m having trouble running the Mac OSX version. It doesn’t seem to be executable. (answer provided by M Neville) The “PHASE.hqx” file seems to have lost its executable permission. In a Terminal window and in the directory with the program type ls -al you should get something like -rwxr-xr-x if the program is executable. If like I did for the extracted PHASE.hqx file yo
