📑 Table of Contents▼
BAM file format
Filename extension
.bam
Developed by
Type of formatBioinformatics
Extended fromTab-separated values
Websitesamtools.github.io/hts-specs/

The BAM file format (which stands for Binary Alignment Map) is the comprehensive raw data of genome sequencing.[2] It consists of the lossless, compressed binary representation of a set of Sequence Alignment Map files.[3][4]

Schema

edit

BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments.[5] The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them. Before indexing, BAM must be sorted by reference ID and then leftmost coordinate.[1] BAM is in compressed BGZF format.

The BAM format; image from: https://samtools.github.io/hts-specs/SAMv1.pdf

The structure of BAM files include a header section and an alignment section:[6]

  • Header—The sample name, sample length, and alignment method are all included in this section. The alignments section contains alignments that are linked to specific information in the header section.
  • Alignments—The read name, read sequence, read quality, alignment information, and custom tags are all included in this file. The chromosome, start coordinate, alignment quality, and match descriptor string are all included in the read name.
    • Alignment Section includes the following:
      • Read Group (RG)
      • Barcode Tag (BC)
      • Single-end alignment quality (SM)
      • Paired-end alignment quality (AS)
      • Edit distance tag (NM)
      • Amplicon name tag (XN)

BAM format uses 0-based coordinate system, where as SAM uses 1-based coordinate system. BAM can represent values in the range [−2^31 , 2^32).[1]

Tools

edit

To view a list of sequencing and analysis tools that work with SAM/BAM click here.

See also

edit
edit

References

edit
  1. ^ a b c "Sequence Alignment/Map Format Specification" (PDF). The SAM/BAM Format Specification Working Group. 3 Jun 2021.
  2. ^ "Carl Zimmer's Game of Genomes, Season 1: Episode 3, BAM Reveals All". STAT. 11 July 2016. Retrieved 2016-08-21.
  3. ^ Li, Heng (2009-06-08). "The Sequence Alignment/Map format and SAMtools" (PDF). Bioinformatics. 25 (16): 2078–9. doi:10.1093/bioinformatics/btp352. PMC 2723002. PMID 19505943.
  4. ^ "Binary Alignment Map". National Cancer Institute Wiki. Archived from the original on August 28, 2016. Retrieved 2016-08-21.
  5. ^ "Genome Browser BAM Track Format". genome.ucsc.edu. Retrieved 2022-05-05.
  6. ^ "BAM File Format". support.illumina.com. Retrieved 2022-05-05.

📚 Artikel Terkait di Wikipedia

SAMtools

post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li

SAM (file format)

an alignment section. The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation

CRAM (file format)

efficient reference-based alternative to the Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) file formats. It optionally uses a genomic reference

Ötzi

subclades downstreaming from G-L91; however, an analysis of his Binary Alignment Map file revealed that he belongs to the L166 and FGC5672 subclades below

Bioconductor

results stored in standard formats like SAM (Sequence Alignment Map) or BAM (Binary Alignment Map) files . Bioconductor supports to integrate miRBase data

List of file formats

structures, genomes, and PubMed records. BAM – Binary Alignment/Map format (compressed SAM format) BCF – Binary compressed VCF format BED – The browser extensible

Data structure alignment

structure alignment is the way data is arranged and accessed in computer memory. It consists of three separate but related issues: data alignment, data structure

Bam

attenuation monitoring, for measurement of particle content in gas flow Binary Alignment Map, the comprehensive raw data from genome sequencing (includes BAM