The display and interpretation of large sets of DNA polymorphism data
can be simplified by using a graphical display. We have found it useful
to present complete raw datasets of indiviudals' genotype data using a display
format called a visual genotype (
VG
) (see Nickerson et al., Nature Genetics, 19:233-240, 1998, and Rieder
et al., Nature Genetics, 22:59-60, 1999). We have adopted this
same format to the display of theoretical haplotype data which is computationally inferred from genotype data. Similar to visual genotype data, we have
adapted this format to present data in an array of samples (rows) x polymorphic
sites (columns) and encodes each polymorphism found on a chromosome
according to a general color scheme where:
- blue = common allele
- yellow = homozygous genotype for the rare allele
- gray = missing data (N)
This array format allows one to visually inspect the data
across both individual's haplotypes and polymorphic sites to make comparisons.
In many cases, presenting data in this visual haplotype format one
can see the result of recombination which has transferred blocks of chromosomal
segments between haplotypes.
We have established a specific format for the uploading of haplotype data.
See below
for complete formatting guidelines.
Displaying Your Own Data
Using this page you are able to upload a file (using the browse button to
find a file on your own computer) and have a visual haplotype produced.
This image will appear in a separate browser window.
Displaying PGA Finished Data
You are also able to directly view data from our
Finished Genes
list and interactively display these visual genotypes. Select the "PGA
Finished Gene Phasebase Input File" button and use the drop-down list to
select a gene.
Display Options
The format of the visual haplotype can be adjusted by filtering out polymorphic
sites below a minimum allele frequency. This is simply done by entering
your minimum cutoff in the "Rare Allele Percentage" box. Haplotypes
can also be sorted (by individual sample or haplotype frequency) or clustered
based on sample or site similarity.
Formatting Guidelines
Haplotype Data Format:
This data formatting has been adapted from genotype data format. In
order to accomodate haplotype data we have a duplicate haplotype allele entry
for each line (which similates a single allele).
This file must be a tab-delimited file with
four fields on each line, in the format:
<Site Position><tab><Sample ID><tab><Haplotype
1 Allele><tab><Haplotype 1 Allele>
<Site Position><tab><Sample ID><tab><Haplotype
2 Allele><tab><Haplotype 2 Allele>
e.g.
200 IND1 A A
200 IND1 G G
These lines would represent two haplotypes
- one having an "A" allele and the other having a "G" allele at position
200, from a sample named IND1. This format must be repeated on each line
of your input file for *all* samples (i.e. two lines per sample) listed in
your input file. If you do not have a haplotype allele for a sample at a
specific site, it would be entered with a genotype of "N N").
Multiple Site Example:
200 IND1 A A
200 IND1 G G
200 IND2 G G
200 IND2 C C
200 IND3 C C
200 IND3 T T
(etc. for more sites)
If you have questions about the data format please see our
Finished Genes
page, and select a gene and view the Individual Genotypes file.
How to Save A Visual Haplotype Image
- Move the mouse pointer over the image you wish to save.
- Press right mouse button.
- Move the pointer over "Save Image As..." (Netscape) or "Save Picture
As..." (Internet Explorer)
- Choose target directory to save to and type-in desired filename.
- Click "Ok" button.
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