text: user15643: I used bwa mem to align the DNA with the reference genome. If there are split reads (chimeric reads, come from two different parts of the genome), will it be split into two lines rather than one line?
  
  user9999: I'm assuming you mean supplementary/chimeric alignment? The SAM Format Specification has a really detailed explanation as well as its Optional Fields Specification.
  In general though, you will have an additional line in the SAM file to represent a chimeric alignment yes. For a single read, one line will represent the primary alignment; this is arbitrarily chosen. The other line will represent the split/supplementary alignment and have its supplementary alignment flag set. If there are multiple chimeric alignments, each one will have its own line.
  You check if a primary alignment has any supplementary alignments associated to it by checking the SA tag which will list the location(s) of any supplementary alignment(s).
  
original_text: 15643: <p>I used bwa mem to align the DNA with the reference genome. If there are split reads (chimeric reads, come from two different parts of the genome), will it be split into two lines rather than one line?</p>
   9999: <p>I'm assuming you mean supplementary/chimeric alignment? The <a href="https://samtools.github.io/hts-specs/SAMv1.pdf" rel="nofollow noreferrer">SAM Format Specification</a> has a really detailed explanation as well as its <a href="https://samtools.github.io/hts-specs/SAMtags.pdf" rel="nofollow noreferrer">Optional Fields Specification</a>.</p>
  <p>In general though, you will have an additional line in the SAM file to represent a chimeric alignment yes. For a single read, one line will represent the primary alignment; this is arbitrarily chosen. The other line will represent the split/supplementary alignment and have its supplementary alignment flag set. If there are multiple chimeric alignments, each one will have its own line.</p>
  <p>You check if a primary alignment has any supplementary alignments associated to it by checking the SA tag which will list the location(s) of any supplementary alignment(s).</p>
  