readme

利用Partition-Ligation algorithm计算生物SNP的单倍型频率

Welcome. Thank you very much for using HAPLOTYPER program.
This program uses Partition-Ligation algorithm to reconstruct 
individual haplotyes from population genotype data.

1. Install

%gunzip haplotyper.tar.gz 
%tar -xvf haplotyper.tar 

The following files contains in this package:
	readme
	htyper
	htyperv2
	input 
	
2. Input

User need to create a file that contains the genotype data 
to be used as an input to the program. The format of the file 
is the follows:
 
1 line for each subject, in each line, 1 digit stands for 1 
SNP, no space in between digits.

All kinds of SNP genotypes are allowed: heterozygous, homozygous 
wild type, homozygous mutant, total missing, one wild type one 
missing and one mutant one missing genotype, we used A/a, A/A, 
a/a, ?/?, A/? and a/? to denote them, (here A denotes wild type, 
a denotes mutant or rare type), and the coding scheme is the follows:

	A/a --> 0
	A/A --> 1
	a/a --> 2
	?/? --> 3
	A/? --> 4
	a/? --> 5

Here is an example:

02102
02121
00220
10233
10102	
 
3. Command
Two programs are enclosed, htyper and htyperv2, htyper can handle 
more SNPs but less people, while htyperv2 can handle more people 
but less SNPs, see Specification section for details. The commands 
are:  

% htyper input output snp people round 
or 
% htyperv2 input output snp people round 

input  : a file contains the genotype information. Any name less
	 than 20 characters long would be fine.
output : a file contains estimated individual haplotypes 
         and haplotype pool information. Any name less than 20 
	 characters long would be fine.
snp    : number of SNPs in the genotype data
people : number of individuals in the genotype data
round  : number of independent runs before report result
 
4. Specification of parameters:

The names of the input and output files should be less than 
20 characters long, otherwise characters longer than 20 
will be ignored.

For htyper:

snp    : integer, 1 ~ 256
people : integer, 1 ~ 100
round  : integer, no limit (recommends 20 or less)

For htyperv2:

snp    : integer, 1 ~ 100
people : integer, 1 ~ 500
round  : integer, no limit (recommends 20 or less)

5. Output 

Output is consist of two parts, individual haplotype 
information and haplotype pool information. In the first 
part, for each subject, the two haplotypes predicted by 
our program is listed, plus the ID number of each haplotype 
in the haplotype pool of this population. The posterior 
probability associated with the selected pair of haplotype 
is also provided, which can be used as a measurement of how 
confident this prediction is accurate.

The second part is the haplotype pool for this population, 
all the haplotypes selected to appear in at least one of 
the subjects are listed. Both the frequency and the percentage 
of appearence in this population are provided. If the SNP 
number is less than 20, we also included a "universal" ID 
number to help identify haplotypes of the same length. This 
feature is particular helpful when one is doing a cross 
platform comparison, like in the classical treatment-control 
setting. This number is the decimal integer number converted 
from the binary code of the haplotype sequence under our 
(0-wild, 1-mutant or rare coding scheme). hence it is unique
for fixed number of marker loci.  

6. Credit 

This program is developed based on algorithm proposed in 
Niu, Qin, Xu and Liu (2001) "In silico Haplotype Determination 
of a Vast Set of Single Nucleotide Polymorphisms." Technical 
report, Department of Statistics, Harvard University. Please 
cite this paper if you used this program in your research for 
publication.
 
7. Support 

All questions and comments should be direct to Steve Qin at the 
Department of Statistics, Harvard University, Cambridge, MA 02138.
Email: [e-mail]