Configuring VCF tracks
| Genome Browser VCF tracks may be configured in a variety of ways to highlight different aspects of the displayed information. Click here for more information on VCF custom track creation. The following configuration options appear only if the VCF file contains genotype columns for at least two samples (four haplotypes): Enable Haplotype sorting display: If checked, then each sample's phased and/or homozygous genotypes are split into haplotypes, clustered by similarity around a central variant, and sorted for display by their position in the clustering tree. The tree (or as much of the tree as space allows) is drawn in the label area next to the track image. If unchecked, then the display is the same as for VCF without genotypes: a stacked bar graph of the top two alleles, showing the proportion of alleles if allele counts are available. This is checked (enabled) by default. The following options are applicable only when enabled. Haplotype sorting order: Haplotypes are sorted using a distance function that uses a central variant; differences between haplotypes are penalized with weights that decrease for each successive variant away from the central variant. By default, the median variant in the window is used. By clicking on a variant in the display, you will get the option to always use that variant when it is in the current view. Color sorted haplotypes by: By default, the reference allele is colored blue and the alternate allele is colored red. This can be changed to the same color scheme used when there are no genotypes: A is red, C is blue, G is green and T is magenta. Haplotype sorting display height:Height in pixels of the haplotype sorting display. If this is fewer than the number of haplotypes (2 * the number of genotype columns), multiple haplotypes may be compressed into a single horizontal pixel row. When the default red/blue coloring is in effect, pixels may be colored purple where the haplotypes differ. Exclude items with QUAL score less than N: If the checkbox is checked, then all records whose QUAL column has a non-numeric value (e.g. ".") or a value less than N are excluded from display. By default, the checkbox is not checked and N is 0. Exclude items with these FILTER values: If the VCF header defines any FILTER codes, then there is a checkbox for each code. If checked, then all records with that code in the FILTER column are excluded from display. By default, no checkboxes are checked, so all records are displayed regardless of FILTER column values. When you have finished making your configuration changes, click the Submit button to return to the annotation track display page. |