Many people are getting their genotypes done by companies such as 23 and Me, ancestry.com, and others.

However, one problem is that people do not have a good understanding of what the data really mean.

Let's add some new capability to IGB that will allow them to open their results files in IGB and then use IGB to learn about genetics.

A typical session would look like this:

• User gets their "raw" data from the genotyping company (typically some kind of plain text file)
• User clicks on the version of the reference human genome associated with the file. Depending on the company, usually this is H_sapiens_Feb_2009 - not the latest one! The user will have know which version it is to proceed!
• User opens their file in IGB. IGB then shows a new empty track.
• User then searches for a gene of interest, e.g., BRCA1, the so-called "breast cancer gene."
• They zoom and pan to the gene of interest - by double-clicking results in Advanced Search or using the Quick search box
• User then clicks "Load Data"

At that point, all the genotype results mapping to the region in view will load. Users will then see a bunch of new items in their genotype results track.

The results will look like rectangles that are maybe 21 bases long. The center of the rectangle can show a diamond or other shape that indicates something about the result. One either side, there will be two "wings" that make it easy for the user to select or interact with the result. Color can be used to indicate aspects of the result, as well. Key things we should show them are: Is the location homozygous or heterozygous? What alleles (bases) are present at each position? Also, what is the identifier of the location, e.g, the "rs id"? What we show will depend a lot on what the genotyping provider puts into the file as well as what we can easily grab from the internet via REST services and that type of thing. For example, we might want to include some REST queries in the code that loads the file. And of course we would want to link out to external sites such as SNPedia so that people can dig deeper into their results.

Let's start with 23 and Me data, since we are already pretty familiar with these data from working on the 23 and Me App - https://bitbucket.org/lorainelab/23andme-snp-converter

See that repository's test/resources directory for a sample file.

Documentation about the data file format:
https://customercare.23andme.com/hc/en-us/articles/115004459928-Raw-Genotype-Data-Technical-Details

The documentation does not say this, but the coordinates listed in the file are one-based. So to convert to IGB coordinates, subtract one.
See also:
https://bitbucket.org/lorainelab/23andme-snp-converter/src/master/src/main/java/org/lorainelab/igb/snp/convert/beans/Bed.java