Data Quality Checks
After loading a file, Haploview shows some basic dataquality checks for the markers. Markers are filtered outbased on some default criteria which can be adjusted asnecessary. Markers can be added or removed from analyses byhand via the checkboxes. The data in this table can besorted by clicking on any of the column headers. Compoundsorts can be done by clicking on the first column headerthen CTRL clicking on the next one.
- # is the marker number.
- Name is the marker ID specified (only if an info file is loaded).
- Position is the marker position specified (only if an info file is loaded).
- ObsHET is the marker's observed heterozygosity.
- PredHET is the marker's predicted heterozygosity (i.e. 2*MAF*(1-MAF)).
- HWpval is the Hardy-Weinberg equilibrium p value, which is the probability that its deviation from H-W equilibrium could be explained by chance.
- %Geno is the percentage of non-missing genotypes for this marker.
- FamTrio is the number of fully genotyped family trios for this marker (0 for datasets with unrelated individuals).
- MendErr is the number of observed Mendelian inheritance errors (0 for datasets with unrelated individuals).
- MAF is the minor allele frequency (using founders only) for this marker.
- Alleles are the major and minor alleles for this marker.
- Rating is checked if the marker passes all the tests and unchecked if it fails one or more tests (highlighted in red).
You can adjust the filtering thresholds and click "Rescore"to refilter the markers using the new values. These thresholdscan be reset to values by clicking "Reset Values". Markers canalso be selected/unselected by hand by clicking the "Rating"checkbox or using the "Select All" and "Deselect All" buttons.Any marker which fails one of the quality tests will have the relevant field(s) highlighted in red.
If two markers in an input file have the same chromosomalposition, Haploview will ignore the less completelygenotyped marker by default and highlight both in yellow onthe check markers panel. When running in nogui modeHaploview always ignores the less completely genotypedversion of two markers with the same position. If you wantto use both from the command line, you'll need to adjust oneof the positions.
If two markers in an input file have the same name, Haploview renamesthe second one in the file by appending ".X" to the filename, where "X"is a running integer count starting with 1. So if you have marker1,marker1 and marker2, Haploview would adjust this to: marker1, marker1.1and marker2. Note that if the markers with the same name have differentpositions, Haploview won't deselect any of them; if they do haveidentical positions, it will filter all but one out as described above.
The top of the tab contains information about individualsfiltered during the loading of the file. It will showoverview information about the number of singletons andtrios used and the number of independent familiesloaded. Further information can be shown by clicking the"Advanced Views" button. This will present a list of up tofour buttons depending on the nature of the loaded dataset.The "Individual Summary" button will show genotyping percentageby family and individual. If individuals have been excluded,the "Excluded Individuals" button will present a list ofexcluded individuals as well as the reason for exclusion.If Mendel errors are present, view detailed Mendel error informationby clicking the "Mendel Errors" button. If male heterozygotesare present in x chromosome data, information about them can be viewedby clicking "Male Heterozygotes". All of these advanced viewscan also be exported using the "Export to File" button. Detailsabout individual filtering can be found in the FAQ.