Answers.Body: <p>The MD string doesn't apply to soft or hard clipped regions,. so your example read becomes <code>43G42</code>. Since variant calling using something simplistic like this is only ever going to use the aligned portion, I guess there was never much reason to bother with adding in soft-clipping information. This also means that you need to parse the CIGAR string if you're using the MD string.</p>
  
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Answers.CreationDate: 2017-06-13T16:50:57.050Z
Answers.LastActivityDate: 2017-06-13T17:01:26.013Z
Answers.LastEditDate: 2017-06-13T17:01:26.013Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I am trying to understand how the MD:Z tag is used. The following is from the <a href="https://samtools.github.io/hts-specs/SAMtags.pdf" rel="noreferrer">SAM Optional Fields Specification</a>, which gives an example but is not thorough. </p>
  
  <blockquote>
    <p>The MD field aims to achieve SNP/indel calling without looking at the
    reference. For example, a string ‘10A5^AC6’ means from the leftmost
    reference base in the alignment, there are 10 matches followed by an A
    on the reference which is different from the aligned read base; the
    next 5 reference bases are matches followed by a 2bp deletion from the
    reference; the deleted sequence is AC; the last 6 bases are matches.
    The MD field ought to match the CIGAR string.</p>
  </blockquote>
  
  <p>Suppose I have a read that I want to soft clip at both ends. If the read starts with CIGAR <code>100M</code> and MD <code>50G49</code>, and I want to change the CIGAR to <code>7S86M7S</code>, what should the MD field become? </p>
  
  <p>Is there a more complete explanation of what appears in the MD tag field?</p>
  
Tags: <file-formats><sam><cigar>
Title: How should the SAM MD tag match the CIGAR string?
ThreadText: # How should the SAM MD tag match the CIGAR string?
  
  (Asked by: username_0 on 2017-06-13)
  
  I am trying to understand how the MD:Z tag is used. The following is from the [SAM Optional Fields Specification](https://samtools.github.io/hts-specs/SAMtags.pdf), which gives an example but is not thorough.
  
  > The MD field aims to achieve SNP/indel calling without looking at the
  > reference. For example, a string ‘10A5^AC6’ means from the leftmost
  > reference base in the alignment, there are 10 matches followed by an A
  > on the reference which is different from the aligned read base; the
  > next 5 reference bases are matches followed by a 2bp deletion from the
  > reference; the deleted sequence is AC; the last 6 bases are matches.
  > The MD field ought to match the CIGAR string.
  
  Suppose I have a read that I want to soft clip at both ends. If the read starts with CIGAR `100M` and MD `50G49`, and I want to change the CIGAR to `7S86M7S`, what should the MD field become?
  
  Is there a more complete explanation of what appears in the MD tag field?
  
  **Tags:** file-formats, sam, cigar
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-06-13. Score: 5
  
  The MD string doesn't apply to soft or hard clipped regions,. so your example read becomes `43G42`. Since variant calling using something simplistic like this is only ever going to use the aligned portion, I guess there was never much reason to bother with adding in soft-clipping information. This also means that you need to parse the CIGAR string if you're using the MD string.
  
  
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