Abstract
BackgroundSAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.FindingsThe first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.ConclusionBoth SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.
Highlights
SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data
In this article we describe the status, new features, and developments in SAMtools and BCFtools
SAMtools and BCFtools represent a unique collection of tools useful for processing and analysis of sequencing data
Summary
Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. In practice, the binary counterparts BAM or CRAM are used for alignment data and, when parsing of large VCF files becomes prohibitively slow, BCF provides a more efficient format for processing variation data.
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