HumanOmni2.5-4v1_H_map_deCODE_b37_2011-05-11.txt
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The genetic map for Alohomora was adapted from the file "HumanOmni2.5-4v1_H_Physical-and-Genetic-Coordinates.txt" (date: 2011-05-11)
available on http://support.illumina.com/downloads/humanomni25-quad_product_support_files.ilmn.

From 2443175 markers on the array 7883 were zeroed out (no physical position was given).
Doubled markers (same position, but different names) were merged. If one of them had a RS-number, this marker was selected.
Chromosome numbering: X-23, XY-24, Y-25, MT-26
Genetic positions for the pseudoautosomal region XY were not given by Illumina.
For the XY region genetic positions were set as 1cM = 1Mb.


ALLELE FREQUENCY FILE
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An allele frequency file for Alohomora is not available here.
On the Illumina support webpage allele frequencies are given as minor allele frequency (MAF).
They don't link the minor allele frequency with a special allele.

How to create an Alohomora allele frequency file?
1. If you have enough unrelated individuals (30 or more) you can calculate the allele frequencies from your data set with ALOHOMORA: 
	"Utilities -> Calculate allele frequencies, callrate, HWE...".  
	The output file can be used as allele frequency file the next time you start Alohomora. (If you start Alohomora to load the data the first time, you can use a dummy/empty allele frequency file.)

2. Calculate the allele frequencies from the 1000Genomes data:
a) Export your data set, code alleles according to the forward strand.
b) Export your data set, coded as A/B alleles
c) Check for each marker which fwd-strand allele is recoded as A (and which is B).
d) Then get the A-allele frequency from the 1000 Genomes.



Franz Rueschendorf, 2014-04-29