SingleIndividualHaplotyper(SIH) - Efficient heuristic algorithms for the SIH problem Version 1.0.0 (15/06/11)

This package contains implementations of eight different algorithms for to solve the Single Individual Haplotyping (SIH) problem. By default it runs ReFHap, which is a very efficient and accurate algorithm to assemble haplotypes from different kinds of fragment data.

Building SingleIndividualHaplotyper

SingleIndividualHaplotyper has been compiled and run successfully on the standard jdk version 1.6.0. To build the distribution library sih.jar on a command line environment run the following commands in the directory where RefHap is located:

cd SingleIndividualHaplotyper
make all

Running SingleIndividualHaplotyper

The front class of SingleIndividualHaplotyper is mpg.molgen.sih.main.SIH and on default settings calls the ReFHap algorithm for haplotyping. Basic usage just requires a file with the description of the fragments (the format is explained below) and the path for the output file. The full usage is as follows:

Usage: 

java -cp SIH.jar mpg.molgen.sih.main.SIH <OPTIONS> <INPUT_FILE> <OUTPUT_FILE>

OPTIONS:
		-v FILE			: Text file with genomic coordinates of variants. By default it assumes that 
							coordinates are located in the first column
		-c INT			: Column in the variants file where coordinates are located. Fields in this 
							column must be integers. 
		-a STRING		: Name of the algorithm to run. Options are Refhap, DGS, and FastHare. SHRThree, 
							Speedhap, TwoDMEC, and WMLF are also supported although they are in general less accurate

The input file is a text file with one line per fragment. Since fragments are allowed to have gaps, each fragment must be divided in segments of continuous calls. The first field is the number of such segments. The second field is the id of the fragment. Two fields are then added for each subfragment, the first is the one based relative start of the subfragment and the second is a binary string with the calls. For HapCUT users, the format is the same as HapCUT. A sample file is provided with this distribution.

The output is a tab delimited text file with the list of blocks. Each block has a header with the one based relative position of the first variant, the size of the block and the number of variants phased. Then, there is one line per variant with the following fields:

• Relative position of the variant
• Allele in the first haplotype
• Allele in the second haplotype

If a file is provided with genomic locations of variants through the -v option, then the relative positions are replaced with the positions contained in this file.

Example 1. Simple usage:

java -cp SIH.jar mpg.molgen.sih.main.SIH example.frags example1.phase

Example 2. Including genomic coordinates

java -cp SIH.jar mpg.molgen.sih.main.SIH -v example.allvars -c 2 example.frags example2.phase

Example 3. Running an algorithm different than ReFHap

java -cp SIH.jar mpg.molgen.sih.main.SIH -a DGS -v example.allvars -c 2 example.frags example3.phase

License

SingleIndividualHaplotyper is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

SingleIndividualHaplotyper is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with SingleIndividualHaplotyper. If not, see http://www.gnu.org/licenses/.