Accurately identifying DNA polymorphisms can bridge the gap between phenotypes and genotypes and is essential for molecular marker assisted genetic studies.Genome complexities,including large-scale structural variations,bring great challenges to bioinformatic analysis for obtaining high-confidence genomic variants,as sequence differences between non-allelic loci of two or more genomes can be misinterpreted as polymorphisms.It is important to correctly filter out artificial variants to avoid false genotyping or estimation of allele frequencies.Here,we present an efficient and effective framework,inGAP-family,to discover,filter,and visualize DNA polymor-phisms and structural variants(SVs)from alignment of short reads.Applying this method to poly-morphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points as well as causal mutations in mutant gen-omes or quantitative trait loci.In addition,inGAP-family provides a user-friendly graphical inter-face for detecting polymorphisms and SVs,further evaluating predicted variants and identifying mutations related to genotypes.