Question: IonTorrent variant calling: "Missing ZM: tags"
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gravatar for graeme.thorn
10 weeks ago by
graeme.thorn30
London, United Kingdom
graeme.thorn30 wrote:

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?

variants ion-torrent • 151 views
ADD COMMENTlink modified 9 weeks ago • written 10 weeks ago by graeme.thorn30

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

ADD REPLYlink written 10 weeks ago by b.nota5.5k

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

ADD REPLYlink written 9 weeks ago by graeme.thorn30
1
gravatar for graeme.thorn
9 weeks ago by
graeme.thorn30
London, United Kingdom
graeme.thorn30 wrote:

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.

ADD COMMENTlink written 9 weeks ago by graeme.thorn30
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