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 20 samples out of ~150) the variant caller stops due to what it states are 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?
1 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.
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Did you call Thermofisher for support? It is commercial software right? They can at least give support for the money they got from you.
Did do, finally, after fruitless searching - it turns out the files need reanalysing from the start, so raw sequencing to BAM needs redoing before calling variant caller