genome_partition's Introduction

genome_partition

partition genome into blocks according to Four Gamete Test

it takes haplotype or genotype data (see SampleData.txt) as input, and find blocks according to Fout Gamete Test.

outputs include: 	BLOCKS	|	CORES	|	SUSPECT SNPS	|	MAXIMAL-K-COVER

our blocks satisfy the following condition:
	A.	no recombination occurs within a block
	B.	every block is a maximal length local Perfect Phelogeny Tree
	C.	allowing overlap between blocks
	Biological meaning: each block contains several SNPs and inherits as a whole unit, which could be directly used to association study, infering genome history etc.
	
our cores satisfy the following condition:
	A.	in dependent of the scanning order (Left-to-Right or Right-to-Left)
	B.	the number of cores is the minimal number of blocks to cover the entire dataset
	C.	no recombination occurs within a core
	D.	no overlap between cores
	Biological meaning: need to be elucidated
	
our suspect SNPs satisfy the following condition:
	A.	once removed, the minimal number of blocks to cover the entire dataset will reduce
	Biological meaning: they are indication of genotyping error, gene conversion and homoplasy.
	
our maximal-k-cover satisfies the following condition:
	A.	it is a set of blocks that are maximal in their overlap and minimal in their number to cover the entire dataset
	Biological meaning: need to be elucidated

to test use: python genotypeScan_sample_usage.py genSampleData.txt python haplotypeScan_sample_usage.py hapSampleData.txt

Recommend Projects