This section generates a properly formatted and ready-to-use file that you
can use as an input file for the Phase software*:
What you need to do is as follows:
1. Enter a Description to identify the process in the top box.
2. Select which of the SNPs in your Study
are going to be used. You can do it
in several ways:
- By position: You can specify a chromosome and a begin and end
positions which delimit a region you are interested in.
- By Region: Depending on the content of the field "Region" in your SNPs Table.
- By Gene: Depending on the content of the field "Gene" in your SNPs
3. If the "Case Control" box is ticked, the Phase input file generated by SNPator will be ready to be run with the Case/Control option on. In this case
the field that will be used to distinguish cases from controls must be selected:
- Then, you have to select a value for cases and controls:
Samples with values other than the ones declared here will be
discarded and not used in the process.
When more than two possible values exist in a field. You may want to
enter only one of those values in either the "Case" or the "Control"
boxes, leaving the other box untouched (that is, leaving the "[Select
Item]" option there). By doing so, those samples that match your
explicit selection are being defined as, say, Cases (or Controls, if you
selected so). All the remaining samples having other values will be
used as Controls.
If a blank is selected " ", that means that there are Samples with no
value in the field and that those are being selected as a case or
4. You can choose Batch Mode:
This is a fundamental time-saving feature. Selecting one of the fields in
the Samples or SNP table, SNPator will run this process as many
times as different values are in that fields, using each time only those samples or SNPs that have each of the values. For instance, if you
have defined your samples in the "sex" field as "M" or "W", selecting
"sex" as the attribute of the Sample batch mode will result in having
two runs of PHASE format retrieval, taking separately men and
If you select at the same time sample and SNP batch fields, you are
going to obtain as many runs of the process as all possible
combinations of the values of samples and SNPs in the fields you
5. Finally, the resulting Phase input file is sent to the User Results section. It
will be a *.zip file containing several files:
This is the Phase input file that has to be given to Phase in
order to perform haplotype estimations.
A text file containing the list of SNPs that have been used to
build the phase input file. It provides info on:
- SNP code
- Distance to next SNP
Another SNP info text with a format suitable for some programs.
SNPator information to identify the job: date, time, user, study
Report of possible errors in the process.
- Haploid data treatment.
When haploid data are used in this section, three scenarios are possible:
* If all genotypes are haploid.
Haplotype estimation does not make sense. An error message
appears and no action is taken.
* If some samples have diploid genotypes, while other samples have
This could be the case of Genotypes coming from the X chromosome.
Diploid samples are treated as usual. The genotypes of haploid samples are duplicated.
* Haploid and diploid genotypes are mixed in the same samples.
An error message appears and no action is taken.
- Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian methods for haplotype
reconstruction from population genotype data. American Journal of Human Genetics,