GW-CALL is a Genome-Wide variant CALLer, that calls variants within the genome based on all mappable reads. The package can be download in source code here: gw-call_source_codes. Currently, it is tested on Mac OS and Linux.

usage:	GW-CALL [options]* -r < ref > -s < sam-file > -o < output >

< ref >	A comma-seperated list of fasta files containing the reference genomes.
< sam-file >	The mapped reads to reference genomes in sam format. This file may be generated by mapping tools such as Bowtie, BWA, SOAP2, and etc.
< output >	Name of the output file including genomic variations in Variant Call Format (VCF).

Options:

-h/–help	Shows this manual.
–dir < folder-name >	Path to the folder containing the reference files [default: parent folder of < sam-file >].
–output-dir < folder-name >	Path to the folder containing the output VCF file [default: parent folder of < sam-file >].
–temp < folder-name >	Path to a folder for some temporary files [default: parent folder of < sam-file >].
–dip	Run in diploid mode.
-d < int >	Maximum hamming distance between the reference and the target sequences corresponding to a cover set [default: 2].
-e < real >	SNV probability [default: 0.001].
-p < real >	Noise probability of reads [default: 0.01].
-k < int >	Size of list decoder for chunks [default: 2].
-i < int >	Number of iterations of dynamic programming on chunks [default: 2].
-m < int >	Maximum number of positions which each read can be mapped [default: 30].
-c < int >	Maximum clique size of clusters for running exhaustive search [default: 20].