SAM/BAM

 This document describes the SAM/BAM file format that GenomeJack supports. GenomeJack uses the sam-1.89 (http://picard.sourceforge.net/) in processing SAM/BAM files.
Reference URL:
Note:
  1. H of CIGAR is not displayed as a hard clipping.
  2. S of CIGAR is not displayed as a soft clipping.
  3. D of CIGAR is displayed as a deletion.
  4. I of CIGAR is displayed as an insertion.
  5. If there is no “SQ” tag in header, the data cannot be sorted. Please read I want to add header information in SAM file. .