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]. |