IonTorrent variant calling: "Missing ZM: tags"

Question

[graeme.thorn]

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?

[Benn]

Did you call Thermofisher for support? It is commercial software right? They can at least give support for the money they got from you.

[graeme.thorn]

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

Answer 1

[graeme.thorn]

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.