Frequently Asked Questions

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How to modify the default folder for genetic maps and allele frequency files?

a) to change the path/name of a single map- or frequency-file: 
- start Alohomora
- select your chip type
- Menu->Options->File selection
	use Browse Button to change the file/path
- press OK Button to close the File selection window
- Menu->Utilities->Save current environment
	this will save the path in alohomora.ini



b) to change the default folder of all map- and frequency-files:
- start Alohomora
- Menu->Utilities->Save current environment
	this creates a file alohomora.ini
- close Alohomora

- open alohomora.ini with a Text-Editor
- find and replace all the strings "/usr/local/genetics" 
  with "/home/neil/genetics" (for example)
- save alohomora.ini


the next time you start Alohomora the modified paths 
should be used.


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How to create an allele frequency file from my own data set:

- start Alohomora 
- load data: press button "Read Infiles" (without filters)
- select Menu->Utilities->Calculate allele frequencies,Callrate,HWE
- select between "all individuals", "founders only", ...
- press OK


The selection "all individuals", "founders only",... will use only samples 
defined in the pedfile.pro. SNPs without physical/genetic position will be 
handled as autosomal markers. For X-linked markers only genotypes from females
are used. The output file "alleles_<sampleset>.frq" can directly be used as allele 
frequency file (the next time you start Alohomora), but Alohomora needs only the
first two columns.


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I have data from Affymetrix arrays and want to see the rs-number in my linkage
analysis files:

In the genetic map files, provided on the Alohomora homepage, the second column
is the original  Affymetrix SNP_A-ID and the fifth column is the rs-number.
Do all quality checks with the original markername (also use the original name 
in the skiplist and in the Merlin unlikely genotype detection)!
Before you create the final linkage analysis files select:
Menu -> Alias names  and select rs-number.
Now create the Merlin, Plink,...  data.

For data from Illumina no change is necessary, because the rs-number is the 
original marker name.


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Does ALOHOMORA handle Illumina Chips, for example the Human610-Quadv1?

ALOHOMORA handles every chip type from every company, even when the chip does 
not appear in the Alohomora selection box "Chip". 
You need a genetic map file, an allele frequency file and the genotype file in 
the Alohomora format. Export the Illumina genotypes as "AA", AB" and "BB".

The Alohomora variables "Chip type" and "Options -> File Selection" are only 
placeholders. For example use for the Human610-Quadv1 annotation files the 
Chip type "Illumina" and in "Options -> File selection" for map and allele 
frequency the "Other" variable.


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