Pharmacogenetics of Asthma Treatment

1. The output file will have a header line with marker names - you MUST use the -nh option of SNPHAP!
2. The current version of SNPHAP (1.0) will break badly if your data contains alphanumeric characters +/- as indel markers. SNPHAP on DARTH has been patched to work with indel indicators, but if you're using the original SNPHAP code,you MUST replace +/- with something else for SNPHAP to work properly - but keep this trickery in mind when looking at the haplotypes!!
3. All care, no responsibility. This software is made available without any kind of guarantee of fitness for any purpose whatsoever. It may NOT work correctly. If you miss the Nobel prize because of my mistake, tough. On the other hand, if you win one, an acknowledgement during your acceptance speech would be appreciated. If you detect reproducible errors, please let know urgently.

The gene name can automatically be included in the plot title, and is also used to label the optional SNP Map which is drawn along the diagonal of the LD Plot. You can change the gene name in the gray box below to anything you like:

Input is a standard prettybase file. Use the file dialog to locate the prettybase file you would like to use on your computer.



Alternatively, for this exercise, you can use the following data (or modify it if you would like). This data represents a set of three SNPs (located at position 100, 200, and 300 in the gene). Each SNP has been genotyped in six individuals from two different populations (H001, H002, H003, M001, M002, M003), giving us a total of 18 data points:

IV. Configure Populations

This text area allows you to configure how the LD Plotter will split the samples in the prettybase file into different populations. The field should have one line for each population represented in your dataset. Each line should be a population identifier, followed by a colon, followed by a description of the population:

V. Action

There are three primary modes of operation for this tool:

•  Return htSNP report: This option will return a text-formatted report about the htSNP in the dataset. This option uses the PyBEST algorithm as described ...
•  Return snphap output: This option will format an input file for snphap and run the snphap program, returning the output.
•  Convert only: This option simply reformats the prettybase data specified into an input file for snphap. This is useful for a researcher who has snphap already installed on another, possibly faster, machine.

V. Minimum Posterior Haplotype Probability

• Minraf: You can set an arbitrary threshold for minimum allele frequence. The default value of will not exclude SNPs based on rare allele frequency. If you specify a higher value, SNPs with frequency for the rare allele below this threshold in any population will NOT appear in the plot. More information ...
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• Show all alleles: The default behavior is to use "sparse" notation, in the manner of Johnson, et.al., which replaces common alleles with ".". This option will instead show all of the alleles in a given haplotype.
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• Split haplotypes at locus: This option will split the haplotypes at the indicated locus, in effect treating each locus as two loci. Input? Locus by index, or by offset? Explanation?
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• Replace Indels: Selecting this option will replace insertion/deletion polymorphisms (indels) with the actual allele present, instead of using the characterizations "+" and "-".
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• Download: The download option will indicate that instead of displaying the results in the browser window, you would like to be prompted for a location where the file will be saved on your computer.