text: user1770: I've been running bwa mem -a for alignment, using the -a flag---this will 
  
  output all alignments for SE or unpaired PE
  
  I've noticed in the SAM that there are several alignments with * in the SEQ and QUAL fields. Based on the documentation:
  
  
  SEQ: segment SEQuence. This field can be a ‘*’ when the sequence is not stored. If not a ‘*’, the length of the sequence must equal the
    sum of lengths of M/I/S/=/X operations in CIGAR. An ‘=’ denotes the
    base is identical to the reference base. No assumptions can be made on
    the letter cases.
  QUAL: ASCII of base QUALity plus 33 (same as the quality string in the Sanger FASTQ format). A base quality is the phred-scaled base
    error probability which equals −10 log10 Pr{base is wrong}. This field
    can be a ‘*’ when quality is not stored. If not a ‘*’, SEQ must not be
    a ‘*’ and the length of the quality string ought to equal the length
    of SEQ.
  
  
  it appears the sequence isn't stored. 
  I would strongly prefer to have the sequence in this case. Is there any to direct bwa to output these sequences? 
  
  user964: I don't believe that is an option.  Internally we created a patch and submitted it to BWA however that was 4 years ago and it has not been accepted.
  
original_text: 1770: <p>I've been running <code>bwa mem -a</code> for alignment, using the <code>-a</code> flag---this will </p>
  
  <blockquote>
    <p>output all alignments for SE or unpaired PE</p>
  </blockquote>
  
  <p>I've noticed in the SAM that there are several alignments with <code>*</code> in the <code>SEQ</code> and <code>QUAL</code> fields. Based on the documentation:</p>
  
  <blockquote>
    <ol start="10">
    <li>SEQ: segment SEQuence. This field can be a ‘*’ when the sequence is not stored. If not a ‘*’, the length of the sequence must equal the
    sum of lengths of M/I/S/=/X operations in CIGAR. An ‘=’ denotes the
    base is identical to the reference base. No assumptions can be made on
    the letter cases.</li>
    <li>QUAL: ASCII of base QUALity plus 33 (same as the quality string in the Sanger FASTQ format). A base quality is the phred-scaled base
    error probability which equals −10 log10 Pr{base is wrong}. This field
    can be a ‘*’ when quality is not stored. If not a ‘*’, SEQ must not be
    a ‘*’ and the length of the quality string ought to equal the length
    of SEQ.</li>
    </ol>
  </blockquote>
  
  <p>it appears the sequence isn't stored. </p>
  
  <p>I would strongly prefer to have the sequence in this case. Is there any to direct bwa to output these sequences? </p>
   964: <p>I don't believe that is an option.  Internally we created a <a href="https://github.com/lh3/bwa/pull/36" rel="noreferrer">patch</a> and submitted it to <a href="https://github.com/lh3/bwa" rel="noreferrer">BWA</a> however that was 4 years ago and it has not been accepted.</p>
  