SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. It 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, or even whole-genome sequencing data.

Sample Data

The sample data are generated from a real dataset from chrX.

Reference for ChrX (fasta format): chrX.fa.gz

Input for pool data (bam/sam format): or

Input for individual data (bam/sam format): or

Target regions (bed format): target.bed

Configuration for pool data: test.bam.ini if use or test.sam.ini if use

ChrX annotation of dbSNP132: dbSNP_132.b37.snp.chrX.vcf


It should be noted that the reference file should be matched the aligned data file, that is, the format of reference file should be the same as the one used in aligning raw sequencing data! Otherwise, “ReferenceNotMatchException” would be thrown from PICARD API, from which SNVer calls for piling up. For example, users can check the SAM/BAM header through SAMTools:

samtools view –H test1.bam, which will give

@HD     VN:1.0  GO:none SO:coordinate
@SQ     SN:chrX LN:155270560

If there is no header information in aligned data or the reference length and name are not correct, it would prevent the program from running. If that is the case, we suggest the user redo the mapping to make sure that the reference file is consistent with the header information in aligned data.