I'm having troubles to perform case-control permutation analysis in PHASE 2.1.1. PHASE documentation says that for this test, individuals should be identified by putting "0" or "1" for controls and cases, respectively, followed by space just before the individual's identifier. However, when I run the program in this way, the following error message appears: "Error in input file: more than 2 alleles at SNP locus. Individual = C; Locus = 1, Alleles are: #, L and C". My individuals are identified by #CICL followed by a number. The weird thing is that when a substitute "0 #" or "1 #" by "0#" or "1#", in other words, when I delete the space, the software reads the file normally, but do not performs the permutation test cause it don't identifies cases and controls in the file, but identifies individuals as a single group.
Does anyone already had this same issue and got any suggestion regarding input file preparation? There is some undocumented bug in this test? There is some restriction in the nomenclature of individuals that may be causing this problem? There is any other software option to perform this test after having all individuals' haplotypes identified?
Thanks!
Glauco,
I think that there is no restriction of how you code your samples. I tried to use the same command of yours in my phase input file, it does not worked cuz you used the '-c' in the wrong position, all commands should be informed before the input file name. Try to use PHASE -c ciclvsher.inp ciclvsher.out and let me know if it works.
It looks the input format is incorrect. What kind of format data do you have? If you have PLINK format data, you can try IPGWAS to convert it into PHASE input format.
Yan-Hui Fan, I've prepared my input file using notepad++. The software is reading the input normally and deciphering haplotypes properly, but it doesn't identify case and control groups. Do you think using PLINK or IPGWAS it wouldn't occur?
Thank you!
Glauco,
Could you tell me what is the command that you are using to run Phase?
Have you used the function "-c" to indicate that you input file has case and controls?
Hi, Rafael!
Yes, I've used the "-c" tag to indicate the permutation analysis in the end of the command line. The command used was: PHASE ciclvsher.inp ciclvsher.out -c
Glauco,
I think that there is no restriction of how you code your samples. I tried to use the same command of yours in my phase input file, it does not worked cuz you used the '-c' in the wrong position, all commands should be informed before the input file name. Try to use PHASE -c ciclvsher.inp ciclvsher.out and let me know if it works.
Rafael,
Thank you so much! It worked now. I'm sorry for the beginner question, it's my first time performing haplotype analysis and I had no idea of what were going wrong with my file. In the end, it was a simple problem. Thank you again, Rafael!
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