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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?

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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.

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