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Genotype Filtering by Marker

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7.3 Genotype Filtering by Marker

[Picture]

Figure 35: Genotype Filtering By Marker

The genotype quality assurance filtering dialog (see Figure 35) offers many options for filtering out markers that do not meet user-defined criteria. Markers can be filtered by call rate, minor allele frequency (MAF), or by three measures of Hardy-Weinberg Equilibrium (HWE).

The genotype columns meeting the criteria for filtering can either be inactivated in the original spreadsheet, listed in a filtering results spreadsheet, or both inactivated and listed in a separate spreadsheet. If the filtering results spreadsheet is created by user selection of the “Output spreadsheet with marker statistics and ‘Drop?’ columns” then all of the markers that were not skipped due to having more than two alleles are listed with a “1” in the ‘Drop?’ column. This indicates the marker was dropped based on the selected criteria and a “0” indicates that the marker was not dropped.

The filtering options are separated into two categories, General Statistics Filtering and Hardy-Weinberg Equilibrium (HWE) Filtering. The filtering options for each category are listed below:

  • General Statistics Filtering:
    • Drop if Call Rate: Drops a marker if the call rate meets the specified criteria. Initial default is to drop a marker if the call rate is less than 0.85.
    • Drop if Minor Allele Frequency (MAF): Drops a marker if the MAF meets the specified criteria. Initial default is to drop a marker if the MAF is less than 0.05.
  • Hardy Weinberg Equilibrium (HWE) Filtering:
    Allows the user to select if the filtering is based on all the samples, on cases only or on controls only. This option is only available if a binary column is selected as a dependent variable.
    • Drop if Hardy Weinberg Equilibrium (HWE) P-value: Drops a marker if the HWE p-value meets the specified criteria. The initial default is to drop a marker if the HWE p-value is less than 0.3.
    • Drop if Fisher’s Exact Test for HWE P-value: Drops a marker if the Fisher’s Exact Test for HWE P-value meets the specified criteria. The initial default is to drop a marker if the value is less than 0.3.
    • Drop if Signed HWE R (positive if more homozygous): Drops a marker if the Signed HWE R meets the specified criteria. The initial default is to drop a marker if the value is greater than 0.2.

At least one filtering criteria and at least one action must be selected in the dialog to obtain results. Multiple filtering criteria are allowed at one time. Depending on the stringency of the filtering criteria, it is possible to filter out all of the markers in a dataset. If this is the case, the filtering should be rerun with less stringent criteria.

For more information on how the statistics are calculated see the following sections:

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