What does it mean to index a BAM file?
Table of Contents
What does it mean to index a BAM file?
Bam files can also have a companion file, called an index file. This file has the same name, suffixed with . bai. This file acts like an external table of contents, and allows programs to jump directly to specific parts of the bam file without reading through all of the sequences.
Who wrote samtools?
Heng Li
SAMtools
| Original author(s) | Heng Li |
|---|---|
| Developer(s) | John Marshall and Petr Danecek et al |
| Initial release | 2009 |
| Stable release | 1.12 / September 22, 2020 |
| Repository | github.com/samtools/samtools |
How do I read a BAM file?
For viewing BAM files, an index file must be found in the same directory as the BAM file. The index should be named by appending “. bai” to the BAM file name. If there is no index file, you can use SAMTools to create one (please download SAMTools from http://samtools.sourceforge.net and install locally).
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:
What is a BAM file genome?
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files.
What information is in a BAM file?
A BAM file (*. bam) is the compressed binary version of a SAM file that is used to represent aligned sequences up to 128 Mb. SAM and BAM formats are described in detail at https://samtools.github.io/hts-specs/SAMv1.pdf. BAM files use the file naming format of SampleName_S#.
What information does a BAM file contain?
What do BAM files contain?
A BAM file (*. bam) is the compressed binary version of a SAM file that is used to represent aligned sequences up to 128 Mb.
How install Samtools in Linux?
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:
