SAMtools is a set of utilities for interacting and post-processing short read alignments of DNA sequences in the formats SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM, written by Heng Li. These files are generated as output by short read aligners such as BWA.
Simple and advanced tools are provided that support complex tasks such as variant calling and visualization of alignments, as well as classification, indexing, data extraction and format conversion.