Detection of rare and common variants in next generation sequencing. SNVer call common and rare variants in the analysis of pool or individual next-generation sequencing data.
The program reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained.
Loci with any (low) coverage can be tested and depth of coverage will be quantitatively factored into final significance calculation. SNVer runs very fast, making it feasible for analysis of whole-exome sequencing data.

Usage: java -jar SNVer.jar -i input_dir -n haploids [options]
Inputfile must be generated from SAMtools pileup in current version
-i <input directory>
-n <the number of haploids in each pool>
Options:
-o <output directory (default current directory)>
-e <sequencing error rate (default 0.01)>
-t <allele frequency threshold (default 0.01)>
-q <base quality threshold (default 13)>

Requirements:
* Java

The license of this software is Free, you can free download and free use this calculator software.