Sometimes HapMap samples are included in Plates in order to serve as a
control of the genotyping process. When a Genotype in a plate coincides with
one in the HapMap data (i. e. same sample and SNP name in SNPator and
in HapMap) it is possible to compare them trying to detect possible
SNPator allows the user to do it automatically:
You can select the plate you want to work with using the combo box on your
Selecting All Plates it is possible to find all contradictions in the Study.
Selecting a particular Plate, on the other hand, only will show intraplate
contradictions but will miss contradictions between different Plates.
The Show All option allows you to view all results that have been canceled
in case you wanted to reevaluate them.
The Add Report option will create a report in a text file containing all the
HapMap coherence control information. The Report will be added in the User
The Report Only option will run in background and will create the HapMap
coherence report in the User Results section but no information will be
interactively shown on the screen.
Click the Go button and you get the list of contradictions:
The screen above shows the list of Genotypes for which contradictions have
been detected between SNPator and HapMap data (they were also given to
you in the Plate Report, if the appropriate options were selected).
They are classified into 3 categories:
Genotypes that present contradictions other than the homozygous -
hemizygous pair (i.e A/AA, G/GG etc...)
Genotypes that present contradictions of the homozygous-
Any kind of incoherences (Errors or Warnings) refering to SNPs or
Samples that have been cancelled by the user.
To see them, that is, to see the particular results that happen to be non-
concordant, you must click the Modify option and a new window appears:
The HapMap genotypes appear in the top in red while the user introduced SNPator genotypes are in subsequent green rows.
In this window, one or more Genotypes can be canceled by the user. You
can only cancel those results you have introduced yourself (That is, the
"user" field has to match the current user. This is important. In case several
users are uploading results in the same Study it avoids them messing with
each other's data). By default, Canceled Genotypes will not be taken into
account when performing a HapMap coherence test (except in the case when
they generate notices).