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.
||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).
||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 >].
||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].