![]() BAM files are typically compressed and more efficient for software to work with than SAM. SAM files are human-readable text files, and BAM files are simply their binary equivalent, whilst CRAM files are a restructured column-oriented binary container format. SAM files can be very large (10s of Gigabytes is common), so compression is used to save space. ![]() Both simple and advanced tools are provided, supporting complex tasks like variant calling and alignment viewing as well as sorting, indexing, data extraction and format conversion. These files are generated as output by short read aligners like BWA. SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li.
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