SAM files

introduction

  • SAMtools are a package implementing various functions for post-processing alignments in SAM format, for example, indexing, sorting, variant caller and alignment viewer.

  • Samtools is designed to support all sequence types and aligner and to create a well-defined interface between alignment and downstream alayses, such as assembly.

  • The following is to introduce SAM format:

    1. SAM file is composed of several groups in the format of one header section ("@" is at front) and one alignment section . All lines are TAB ('\t') delimited.
    2. SAM file is consisted of (1)eleven mandatory fields and (2)a variable number of optional fields.

Data infomation

  • Eleven mandatory fields are the following [2]

  • Each item could be further discussed more detailed, for example, the FLAG field [2] as the following :

  • One variable number of optional field is consisted of the following items:
    TAG:TYPE:VALUE
    1. TAG: two characters string matching /[A-Za-z][A-Za-z0-9]/
    2. TYPE: single case-sensitive letter defining the VALUE format.
    3. VALUE: the description

Reference

  1. Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan et al. (2009) The Sequence Alignment/Map format and SAMtools. BIOINFORMATICS Vol. 25 no. 16, pages 2078–2079
  2. The SAM/BAM Format Speci.cation Working Group. (2013) Sequence Alignment/Map Format Specication.
  3. 有勁的生物與資訊. 教學-於 Window 7 平台下使用 samtools 尋找 SNPs / InsertAndDeletions. (2013)

results matching ""

    No results matching ""