The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
An example case use would be to vet putative SNP or INDEL variant calls correlated to a disease phenotype. A researcher would like to make sure that the variants are not do to a sequence artifact or alignment problem. Direct inspection of read alignment against a reference genome could rule this out. An investigator would first select and load one of the many available reference genomes. If not available, IGV provides the user with a means of generated custom genome. Then, the user loads a set of BAM files and then can visually inspect alignment quality.
IGV provides a well-documented and on-line User-guide.
IGV download instructions are provide with link.