|
- If the input files contain different individuals then the program automoatically selects individuals who are present in both files.
For compatibility of IDs across different Cardiff University schizophrenia databases the strings "SZC" and "SCZ1104" are automatically removed from the input files (so take care that your IDs do contain these strings as part of a particular individuals' unique ID).
Note that input file 1 can be the same file as input file 2 if you have all the markers of interest in a single file.
If the markers of interest are in the same file simply load the file in twice in the browse boxes
|
|
- Markers must be diallelic and coded 1 and 2.
|
|
- Missing genotypes must be coded as 0; if one allele is missing then the other alelle must also be missing.
|
|
- The marker names in the header line should not contain spaces or the underscore character "_".
To identify the 2 alleles the program interprets anything after an underscore as the allele coding; e.g. somemarkername_1 somemarkername_2 describes alleles 1 and 2 at marker "somemarkername". Header line entries such as mkname_allele1 mkname_allele2 or mkname_all1 mkname_all2 etc should also work. The different alleles must be labelled differently!
|
|
- The individuals do not have to be included in the same order in the two files
(however if the only difference between the files is the difference in order of individuals then the marker selection page will list all markers twice)
|
|
- Parents will usually be coded as unknown for case-control data; note the program simply ignores the values in the FATHERID and MOTHERID columns.
|
|
- Affected individuals must have a "2" in the AFFECTION_STATUS column and unaffected individuals must have a "1" in the AFFECTION_STATUS column.
|