Samtools Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools Reading/writing/editing/indexing/viewing …

Documentation for BCFtools, SAMtools, and HTSlib’s utilities is available by using man command on the command line. The manual pages for several releases are also included below — be …

Each command has its own man page which can be viewed using e.g. man samtools-view or with a recent GNU man using man samtools view. Below we have a brief summary of syntax and …

SAMtools and BCFtools are distributed as individual packages. The code uses HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

The samtools fixmate tool corrects any flaws in read-pairing that may have been introduced by the aligner. Sadly a number of them have subtle bugs and quirks, so this can be considered as a …

WGS/WES Mapping to Variant Calls The standard workflow for working with DNA sequence data consists of three major steps: Mapping Improvement Variant Calling Mapping For reads from …

Feb 2, 2015 · Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting, …

Samtools is also able to open a BAM (not SAM) file on a remote FTP or HTTP server if the BAM file name starts with `ftp://' or `http://'. Samtools checks the current working directory for the …

Ignored for compatibility with previous samtools versions. Previously this option was required if input was in SAM format, but now the correct format is automatically detected by examining …

Documentation for BCFtools, SAMtools, and HTSlib’s utilities is available by using man command on the command line. The manual pages for the 1.21 release are listed below.