![]() This file will always be much smaller than the BAM file and acts as a “table of contents” for the BAM file, indicating where in the BAM file a specific read or set of reads can be found. The BAM Index FileīAM files are often accompanied by a BAM index file also known as a BAI file with a similar name. Most software that expects a BAM file as an input also expects that BAM file to be sorted, which is why this is often the first step in processing a BAM file. The choice of method will be dependent on the downstream application, but often sorting by coordinate is the correct choice for genomic data. When sorting the BAM file, the two choices for sorting methods will be by sequence identifier, or by genomic coordinates (often referred to as location or position). Sorting of a BAM file can be done by a few different bioinformatics applications, with Samtools and Picard being common programs for this and several other sequence analysis tasks. As a general rule, BAM files should be sorted as a first step to ensure that they are sorted in the way the user thinks they are. As the reads used to generate a BAM file are (or at least should be) random regarding their positions within the genome, and BAM files often start out sorted by read identifier, if they are sorted at all. The two initial steps taken after the generation of a BAM file are to sort and then index it. The remainder of this piece will refer to just the BAM file for simplicity, although the data are identical between SAM and BAM files. Alignment data is almost always stored in BAM files and most software that analyzes aligned reads expects to ingest data in BAM format (often with a BAM index file, to be discussed later in this post). On the other hand, BAM files are smaller and more efficient for software to work with than SAM files, saving time and reducing costs of computation and storage. Since SAM files are a text file format, they are more readable by humans and will be used as the examples for this section.īAM files contain the same information as SAM files, except they are in binary file format which is not readable by humans. These files can also contain unmapped sequences. SAM files are a type of text file format that contains the alignment information of various sequences that are mapped against reference sequences. From these files, with downstream bioinformatics analysis, you can compare gene expression, survey biodiversity, analyze DNA methylation, or investigate DNA-protein interaction, among many other NGS applications. Most bioinformatics tools accept and expect alignment results in BAM format. At their essence, aligners can be expected to take in raw sequence data in the form of a FASTQ along with a reference genome (often in the form of a FASTA file) and generate a new file containing the reads as well as the genomic location from which they originated. There are many different aligners available, with the different types of aligners, their optimal applications, and how they work potentially being the subject of multiple blog posts. Alignment is a common step in many bioinformatics workflows involving nucleic acid sequencing. In bioinformatics, alignment data for large numbers of aligned reads are often output as a sequence alignment and map (SAM) or binary alignment and map (BAM) file. What are SAM & BAM Files? Understanding the SAM & BAM File Format SAM vs.
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