What is SAMtools index?
Table of Contents
What is SAMtools index?
DESCRIPTION. Samtools is a set of utilities that manipulate alignments in the SAM (Sequence Alignment/Map), BAM, and CRAM formats. It converts between the formats, does sorting, merging and indexing, and can retrieve reads in any regions swiftly. Samtools is designed to work on a stream.
How do I view BAM header files?
Inspect the header. The “header” in a BAM file records important information regarding the reference genome to which the reads were aligned, as well as other information about how the BAM has been processed. One can ask the view command to report solely the header by using the -H option.
What is SAMtools merge?
samtools merge – merges multiple sorted files into a single file.
What does the option in samtools view do?
This option saves time spent on compression/decompression and is thus preferred when the output is piped to another samtools command.
What is a BAM header?
BAM files contain a header section and an alignment section: • Header—Contains information about the entire file, such as sample name, sample length, and alignment method. Alignments in the alignments section are associated with specific information in the header section.
How do I compile samtools?
Install samtools on UNIX system
- Download the most current version from the Samtools website.
- Unzip the file: Copy to ClipboardCode BASH :
- Go into the newly created directory and compile the code by typing make: Copy to ClipboardCode BASH :
- Modify your .bashrc file so that when you type “samtools” it calls the program:
What is the latest version of Samtools?
samtools-1.13.tar.bz2. 7.62 MB Jul 07, 2021.
What is BAM header?
Where is Samtools installed?
Installation
- Download the most current version from the Samtools website.
- Unzip the file: Copy to ClipboardCode BASH :
- Go into the newly created directory and compile the code by typing make: Copy to ClipboardCode BASH :
- Modify your .bashrc file so that when you type “samtools” it calls the program:
Does Samtools work on Windows?
In order to install Samtools, first go to the Conda installation link that I mentioned at the beginning of the screencast website: https://docs.conda.io/en/latest/miniconda.html to install the Conda installer for your operating system, Mac, Linux or Windows.
