Answers.Body: <p>It turns out, after speaking to tech support, that these are old files from a previous version of the software so won't run through variant caller.</p>
  
  <p>The files themselves need reanalysing from the initial FASTQ -> BAM with the newest version.</p>
  
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Answers.CreationDate: 2018-10-11T11:12:25.207Z
Answers.LastActivityDate: 2018-10-11T11:12:25.207Z
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Body: <p>I have a lot of IonTorrent sequencing data in BAM format that I want to call variants on, using the IonTorrent variant caller. However, for some of the BAM files (for about 12 samples out of ~150), the variant caller stops due to what it states is lack of ZM: tags in a few individual reads.</p>
  
  <p>The thing is, most of the reads in the BAM file do not have ZM: tags (when viewed through samtools view), but these do not apparently cause problems.</p>
  
  <p>What settings do I need to change to get these BAM files to process, or do I just filter out the problematic reads and analyse the remainder? </p>
  
Tags: <variant-calling>
Title: IonTorrent variant caller failing, lack of ZM: tags in BAM files
ThreadText: # IonTorrent variant caller failing, lack of ZM: tags in BAM files
  
  (Asked by: username_0 on 2018-10-04)
  
  I have a lot of IonTorrent sequencing data in BAM format that I want to call variants on, using the IonTorrent variant caller. However, for some of the BAM files (for about 12 samples out of ~150), the variant caller stops due to what it states is lack of ZM: tags in a few individual reads.
  
  The thing is, most of the reads in the BAM file do not have ZM: tags (when viewed through samtools view), but these do not apparently cause problems.
  
  What settings do I need to change to get these BAM files to process, or do I just filter out the problematic reads and analyse the remainder?
  
  **Tags:** variant-calling
  
  
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  ## 1 answers
  
  ### Answer by username_0 on 2018-10-11. Score: 1 | Accepted answer
  
  It turns out, after speaking to tech support, that these are old files from a previous version of the software so won't run through variant caller.
  
  The files themselves need reanalysing from the initial FASTQ -> BAM with the newest version.
  
  
  ---
  
  