polyHap2 Documentation
Environment Set Up
Java Runtime Environment is required in order to run polyHap2. The latest version of JRE can be downloaded from Sun website. polyHap2 is designed to work with version 1.6.0_01 JRE or later.
To Execute Program
The first step is a data conversion step, which you can run from the example directory using
(1) java –cp ../libs/polyHap2.jar dataFormat.CompressPolyHap2 --paramFile log.txt
This command line will convert your input files (genotype and sample files) to the format which is needed for the polyHap2. This produces a .zip file containing SNP information and a build file.
(2) java –cp ../libs/polyHap2.jar lc1.dp.appl.DickFormat --paramFile log.txt
Note, before executing the main program, make sure the zip file and the build file are included in the same directory.
Input File Format
log file specifies the parameters used in the program, such as input file names,
chromosome name, phasing types (non-internal or internal phasing) ,the SNP
region included for analysis, the number of chromosome (ploidy)....etc. Please
see the detail in the file, ‘log.txt’.
Genotype data file---each row contains information about SNP id and SNPposition and genotypes for each of individuals. Please note that this file should
not have a header line. Each column is separated by a space or tab. At moment
the code only deals with biallelic markers and a deletion. The first two
columns are SNP id and SNP position, respectively. Then, the following
columns are genotypes (one for each individual). For example, a row with 5
individuals from the dataset might look like:
SNP1
1000
GTG G_ TTG TG TG
Ind 1 Ind 2 Ind 3 Ind 4 Ind 5
For each marker, alleles can be coded as any two different letters, apart from
‘N’ which is the code for missing allele. If the number of allele of a missing
genotype, it should be coded as NA’. An example file is shown in ‘genotypeInfo.txt’. Sample file consist of one column for the list of all sample id. The order of this list should be the same as in the genotype file. An example file is shown in ‘sampleID.txt’. Output File phased_states.txt_1: contains the phased ancestral haplotypes (phased states). The first two rows are the number of individuals and SNPs respectively, following by the phased ancestral haplotypes for each of individuals. Each number represents a cluster. One row presents one haplotype. One column is for one marker. Phased2.txt_1: contains the phased genotypes. The first two rows are the number of individuals and SNPs respectively, following by the phased genotypes for each of individuals. Alleles are shown in ‘A’, ‘B’ or _’, where
`A’ presents the first allele shown in the dataset for each SNP. One row
presents one haplotype. One column is for one marker.
Phased1.txt_1: contains certainty rates for each estimate. The first two
columns are SNP id and position respectively. The following columns give the
certainty rate for each of individuals. Each individual has three columns which
are the certainty rate for phased states, phased genotypes, predicted genotypes
(for missing genotype), respectively.