Pharmacogenetics of Asthma Treatment
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Warning - this is a new tool undergoing testing!
This tool will convert a ped format file into a prettybase file suitable for all the tools which require prettybase format data
The input file should have the usual 6 pedigree columns (familyid, individualid, fatherid, motherid, gender, affectedstatus) followed by pairs of alleles for each marker. All fields should be separated by one or more spaces (or one tab character). Note that every record must have the same number of fields.
In the absence of an optional header line (see below), markers are assigned sequential integers as names so it is recommended that you order the markers in their physical/genomic order so tools like LDplots and so on make sense.
The input file may have an optional header line (such as might be used for an excel spreadsheet). Header fields are not permitted to contain any whitespace. The first 6 header fields can be any arbitrary names (these are ignored) and they must be followed by one markername for each allele so there are exactly the same number of header fields as columns - eg
fid iid pid mid gender status 03559_1 03559_2 22233_1 22233_2If you use the optional header, note that every second markername is ignored (since there should be exactly 2 alleles for each marker) and that the name used will be stripped of anything after a _ character - so the above example would give a prettybase file with 2 markers called 03559 and 22233.
There is also an option to use the affectedstatus column as the first character for each individual subject ID. This may be useful if you need to prefix certain ID's and analyse them separately using the tools which require a prettybase file. However, note that in order to use this option, you should ensure that the affectedstatus column contains alphabetic characters - not numbers since all the tools require different letters at the start of ID's in order to distinguish subgroups.
WARNING: Unpredictable but bad things will likely happen if you fail to set the header switch for a .ped file containing a header line or vice versa