# arg4wg
An algorithm to build ancestral recombination graphs for thousands of whole genomes

Citation:
Nguyen, T. T. P., Le, V. S., Ho, H. B., & Le, Q. S. (2017). Building ancestral recombination graphs for whole genomes. IEEE/ACM transactions on computational biology and bioinformatics, 14(2), 478-483.

-------- Instruction to compile and run arg4wg ---------

Requirements:
-	g++
-	gcc

Compilation:
In the ARG4WG folder, type the following command line:
make

Running ARG4WG:
Type ./arg4wg for showing options.

Example:
To build 3 ARGs for data in sample/ folder using 1 thread, the command line is:
./arg4wg –out sample/arg –nthread 1 –narg 3 –data sample/500haps1ksnps sample/500haps.name

We will have 3 ARGs arg0, arg1, arg2.
ARG files have the following format:

Sample NUM_SAMPLES
SAMPLE_NAME_1	SAMPLE_NAME_2	… 	SAMPLE_NAME_NUMSAMPLES
Nodes NUM_NODES
NODE_0_ID	NODE_0_POS_LEFT	NODE_0_POS_RIGHT	NODE_0_PARENT_1	NODE_0_PARENT_2	NODE_0_CHILD_1	NODE_0_CHILD_2
NODE_1_ID	NODE_1_POS_LEFT	NODE_1_POS_RIGHT	NODE_1_PARENT_1	NODE_1_PARENT_2	NODE_1_CHILD_1	NODE_1_CHILD_2
…
NODE_NUMNODES_ID	NODE_ NUMNODES_POS_LEFT	NODE_NUMNODES_POS_RIGHT	NODE_ NUMNODES_PARENT_1	NODE_NUMNODES_PARENT_2	NODE_ NUMNODES_CHILD_1	NODE_NUMNODES_CHILD_2		

Beside ARG, the marginal trees are also output using -tree option. The tree files have the following format:
Marker 0
CHILD1 CHILD2 PARENT
…
Marker 1
CHILD1 CHILD2 PARENT
…
Marker NUMMARKERS
CHILD1 CHILD2 PARENT
…