Coherence Hapmap
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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 genotyping errors.

SNPator allows the user  to do it automatically:

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You can select the plate you want to work with using the combo box on your left:


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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 Results section.

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:

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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:

Errors:

Genotypes that present contradictions other than the homozygous - hemizygous pair (i.e A/AA, G/GG etc...)

Example: AA/AT


Warnings

Genotypes that present contradictions of the homozygous- hemizygous type.

Example: A/AA


Notices

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:


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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).