Haplotype sorting display
When this display mode is enabled and genotypes are phased or homozygous, each genotype is split into two independent haplotypes. These local haplotypes are clustered by similarity around a central variant. Haplotypes are reordered for display using the clustering tree, which is drawn in the left label area. Local haplotype blocks can often be identified using this display.
Enable Haplotype sorting display
| Haplotype sorting order: using middle variant in viewing window as anchor. |
| To anchor the sorting to a particular variant, click on the variant in the genome browser, and then click on the 'Use this variant' button on the next page. |
Haplotype coloring scheme:
reference alleles invisible, alternate alleles in black
reference alleles in blue, alternate alleles in red
first base of allele (A = red, C = blue, G = green, T = magenta)
Haplotype clustering tree leaf shape:
draw leaf clusters as <
draw leaf clusters as [
Haplotype sorting display height:
Filters
Exclude variants with Quality/confidence score (QUAL) score less than
Minimum minor allele frequency (if INFO column includes AF or AC+AN):
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