BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments.[4] 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.[5] BAM is in compressed BGZF format.
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).[5]
To view a list of sequencing and analysis tools that work with SAM/BAM click here.
binary, alignment, comprehensive, data, genome, sequencing, consists, lossless, compressed, binary, representation, sequence, alignment, files, compressed, binary, representation, sequence, alignment, compact, index, able, representation, nucleotide, sequence,. 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 2 3 BAM is the compressed binary representation of SAM Sequence Alignment Map a compact and index able representation of nucleotide sequence alignments 4 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 5 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 5 To view a list of sequencing and analysis tools that work with SAM BAM click here See also editFASTQ format SAM format SAMtools CRAM format List of file formats for molecular biology Compression of Genomic Sequencing DataExternal links editSAM format specification Portal nbsp BiologyReferences edit Carl Zimmer s Game of Genomes Season 1 Episode 3 BAM Reveals All STAT Retrieved 2016 08 21 Li Heng 2009 06 08 The Sequence Alignment Map format and SAMtools PDF Bioinformatics 25 2078 9 doi 10 1093 bioinformatics btp352 PMC 2723002 PMID 19505943 Binary Alignment Map National Cancer Institute Wiki Retrieved 2016 08 21 Genome Browser BAM Track Format genome ucsc edu Retrieved 2022 05 05 a b Sequence Alignment Map Format Specification PDF The SAM BAM Format Specification Working Group 3 Jun 2021 BAM File Format support illumina com Retrieved 2022 05 05 Retrieved from https en wikipedia org w index php title Binary Alignment Map amp oldid 1089412454, wikipedia, wiki, book, books, library,
