#BAM FILE FORMAT COLUMNS SOFTWARE#

The formal descriptions for these columns (and everything) can always be found in the SAM specification. The sequence of ASCII characters encoding the PHRED quality scores for each base of the underlying read The sequence of bases constituting the underlying read Becomes relevant when working with pair-end data. a POS of 100 would indicate the read mapping starts at the 100th position of RNAMEДЄn integer which should be a reflection of the quality of the mapping, but for which the scale and meaning may differ by alignerДЄ string of letters and numbers describing the matches and mismatches of the alignment from left to right. chr1ДЎ-based leftmost mapping position with respect to reference, e.g. Name of the reference to which the read was mapped, e.g. the name of the read which was mapped (copied from the read's FASTQ record header)ДЄn integer which is a short hand way of describing the type of alignment this is. Here's an overview of those, with informal descriptions for each: There is one record per line, and each record consists of a number of tab-separated columns. A SAM record is a description of an alignment (or an unmapped read, if it was unaligned).

The alignment section is where the bulk of the information in the file is stored. However, it is important to remember that the header and the information it contains is optional.

#BAM FILE FORMAT COLUMNS SOFTWARE#

Various command-line tools and software libraries make use of the header section by writing all sorts of meta-data for later use, either by a human manually inspecting the header, or by another tool looking for certain key bits of information. вќ“ By looking at the SAM specification, can you figure out what PG stands for? LN:4641652 which gives us the length of the reference in bases. Thereafter, each entry within a header line follows the format key:value, e.g. For instance, SQ refers to Reference sequence dictionary, which stores info about the reference sequence against which the alignments in this file were made. The first two letters of a header line are known as 'header record type codes', and denote the kind of information each header line will contain. coli K12 reference sequence: SN:U00096.3 ID:minimap2 PN:minimap2 VN:2.17-r941 CL:minimap2 -ax map-ont. Here's an example header, in this case generated from an alignment of the E. If it exists, it can contain any information but is primarily the home of meta data, like SAM versioning info, the commands used to generate the file, or information about the references used in alignment.

The header section naturally precedes the alignment section. Quoting the spec, a SAM file is described as a TAB-delimited text format consisting of a header section, which is optional, and an alignment section. It may look daunting, but its a very clearly laid out document which you can consult with any time you have a question related to SAM formatting. However, before we do, arm yourself with this link to the SAM specification, and keep it handy. With our introduction out of the way, let's dive into what a SAM file looks like.

Most of the tools which operate on SAM files also work on BAM files interchangeably, but equally many tools require BAM instead of SAM. This compression helps reduce the file size significantly. BAM stands for Binary Alignment Map, and is the compressed, binary version of a SAM file.In this tutorial we will introduce the format, provide useful links to tools and documentation, as well as help you to get started with some basic examples of creation and inspection. SAM is an important biological file format, not least because of the extensive ecosystem of tools which require it as input, but also thanks to the range of utilities which make it easy to write, query and transform them. In this tutorial, we'll focus on aligned-SAM files. However, the SAM format is also used to store unaligned nucleotide sequence data, and this is use-case is steadily increasing in popularity. The SAM format) is a file type most commonly used to store the results of nucleotide sequence alignments.

Bam file format columns