Haplotype Frequency Calculation
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11.6 years ago
AsoInfo ▴ 300

Hi there,

I have the data as shown below: (the samples are 200 app.)

SNP1 SNP2 SNP3

A/A C/G T/T

A/C G/G A/T

I have created the haplotypes using the Haploview (Haploview can provide me with the estimated value in percentages) But if, I want to know the exact number of each haplotype in the sample, how can I have that?

Thank You!

haplotype frequency • 12k views
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Is it not frequency(percentages) multiplied by number of samples?

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For example in haplotypes tab, the GCT (0.285) is written, so it means the frequency of GCT is 28.5% (as I have read somewhere - i just have to dig out that article). So how could be the actual number of haplotypes will be 0.285?

I hope I have explained it well :)

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Firstly, without physical phasing, there is no way to know exactly the number of each possible haplotype. Statistical phasing only gives you probabilities, not integer numbers. Secondly, I think zx8754 is quite clear that number=frequency*totalNumber.

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11.6 years ago
zx8754 12k

You can output haplotype frequencies as text file, then have a look at manual for explanation:

Haplotype Text Output File Haplotype output shows a block, its markers, the haplotypes and their population frequencies, the crossover percentages to the next block and the multiallelic D prime. Crossover percentages are shown as a matrix with this block's haplotypes as the rows and the next block'shaplotypes as the columns. An example might look like:

BLOCK 1.  MARKERS: 1 2 3 4
3312 (0.825)    |0.800  0.025   0.000|
1144 (0.163)    |0.031  0.125   0.007|
3342 (0.013)    |0.006  0.000   0.006|
Multiallelic Dprime: 0.802
BLOCK 2.  MARKERS: 10 11 12
441 (0.837)
222 (0.150)
242 (0.013)


In this example, the first block has 4 markers with 3 haplotypes displayed and the second block has 3 markers and 3 haplotypes. The tag SNPs for each block are (3,4) and (10,11) respectively. The crossover percentage matrix can be read as follows: 80% of all samples have the pattern 3312-441, 3.1% have the pattern 1144-441 and so forth.