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SAMtools provides the following commands, each invoked as "samtools some_command".view The view command filters SAM or BAM formatted data. Using options and arguments it understands what data to select (possibly all of it) and passes only that data through.
SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is present. Headings begin with the '@' symbol, which distinguishes them from the alignment section. Alignment sections have 11 mandatory fields, as well as a variable number of optional fields. [1]
www.htslib.org /doc /samtools-mpileup.html Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP /indel calling and alignment.
Bash was the default foreign language. Function application had to be performed using an apply form that took task as its first keyword argument. One year later, this surface syntax was replaced by a streamlined but similar version. The following example script downloads a reference genome from an FTP server.
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files.
They often begin with "Usage:" , the command, followed by a list of arguments. To indicate optional arguments, square brackets are commonly used, and can also be used to group parameters that must be specified together. To indicate required arguments, angled brackets are commonly used, following the same grouping conventions as square brackets.
An input argument (the argument to an input parameter) must be a value, such as an initialized variable or literal, and must not be redefined or assigned to; an output argument must be an assignable variable, but it need not be initialized, any existing value is not accessible, and must be assigned a value; and an input/output argument must be ...
A compound term is composed of an atom called a "functor" and a number of "arguments", which are again terms. Compound terms are ordinarily written as a functor followed by a comma-separated list of argument terms, which is contained in parentheses. The number of arguments is called the term's arity.