text: user2244: 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? 
  
  user2244: 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.
  
original_text: 2244: <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>
   2244: <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>
  