2SNP Phasing Package

2SNP: Phasing Package

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3. Maximum datasize (# of genotypes in your data / # of SNPs in your data)

ON JULY 20, 2007 WE RELEASE NEW VERSION OF 2SNP PACKAGE.

2SNP Phasing Package
version 1.7 +TRIO

IT IS FASTER THAN PREVIOUS VERSIONS, IT CAN PHASE DATA WITH TEN
THOUSANDS SNPs IN A MATTER OF MINUTE. THE MAXIMUM NUMBER OF SNPs
WHICH CAN BE PHASED IS 82K FOR 32-bits ARCHITECTURE and 5000K
FOR 64-bits ARCHITECTURE. IT ALSO HANDLES TRIO DATA AND DATA WITH
TWO TYPES OF MISSING SNP VALUES: BOTH ALLELES ARE UNKNOWN OR ONE
ALLELE IS KNOWN.

SPEED COMPARISON WITH VERSION 1.1:
ON INTEL (32-bit) PROCESSOR 3Ghz, RAM 2Gb, OS LINUX

#GENOTYPES = 30
RUNTIME IS AT MOST LINEAR TO THE NUMBER OF GENOTYPES

#SNPs ver.1.1 ver.1.5

1.5K 60 sec 2 sec

2.5K 270 sec 8 sec

5.0K 2000 sec 25 sec

10.0K - 55 sec

20.0K - 220 sec

40.0K - 17 min

60.0K - 35 min

80.0K - 70 min

PROGRAM SPECIFICATION:

Input parametrs:

input_genotype_file_name
output_Haplotype_file_name

Sample running:

./2snp genotypes.txt haplotypes.txt [-TRIO][-HALFKNOWN]

File formats:

input_genotype_file:
One line per genotype, SNPs values are in {0,1,2,?}
0 - homozygous SNP with major allele
1 - homozygous SNP with minor allele
2 - heterozygous SNP
? - missing data
3 - missing data with one known allele equal to 0
4 - missing data with one known allele equal to 1

-TRIO - parameter for trio data, if missed then data are phased as unrelated
-HALFKNOWN - parameter for missing data with one known allele

For the trio data genotypes should be given in triplets:
FATHER 1
MOTHER 1
CHILD 1
FATHER 2
MOTHER 2
CHILD 2
.......

output_haplotype_file:
Two haplotypes per genotype.
One line per haplotype, SNPs values are in {0,1}
0 - major allele SNP
1 - minor allele SNP

The output haplotypes file for TRIO data has format:

for each TRIO there are 4 haplotypes:

non-transmitted haplotype of FATHER 1
non-transmitted haplotype of MOTHER 1
haplotype of child received from FATHER 1
haplotype of child received from MOTHER 1
.........

Mendelian errors presented in TRIO data are reported in mendel.err

Sample input and output:

The input file genotypes.txt contains 9 genotypes (3 trios) each with 96 SNPs

The output file haplotypes-unrel.txt is a result of phasing by 2SNP of genotypes.txt
as unrelated which contains 18 haplotypes each with 96 SNPs.

The output file haplotypes-trio.txt is a result of phasing by 2SNP of genotypes.txt
as trios which contains 12 haplotypes each with 96 SNPs. File mendel.err traks mendelian errors.

Related articles:

	Brinza, D. and Zelikovsky, A. (2007) `2SNP: Scalable Phasing Method for Trios and Unrelated Individuals', Journal of IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) , 2007.
	Brinza, D. and Zelikovsky, A. (2006) `2SNP: Scalable Phasing Based on 2-SNP Haplotypes', BIOINFORMATICS , pdf Pub 2006 Feb 1;22(3):371-3. Epub 2005 Nov 15.
	Brinza, D. and Zelikovsky, A. (2006) `Phasing of 2-SNP Genotypes based on Non-Random Mating Model', International Workshop on Bioinformatics Research and Applications (IWBRA'06), Proc. of ICCS 2006, LNCS 3992, pp. 767–774, pdf.

Contacts:

Alexander Zelikovsky
Phone: (404) 651-0676
Fax: (815) 642-0052
Email: alexz@cs.gsu.edu
Office: 1443, Peachtree Str. 34
web:http://www.cs.gsu.edu/~cscazz/

Dumitru Brinza
Phone: (858) 822-2496
Email: dima@cs.ucsd.edu
Office: 9500 Gilman Dr., San Diego
web:http://www-cse.ucsd.edu/~dbrinza/

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This code may be freely used for all non-commercial purposes.
(c) Copyright, 2005 by Professor Alexander Zelikovsky
Department of Computer Science, Georgia State University
Atlanta, GA 30303 (404) 651-0676
alexz@cs.gsu.edu http://www.cs.gsu.edu/~cscazz/