Question: IonTorrent variant calling: "Missing ZM: tags"
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gravatar for graeme.thorn
18 days ago by
graeme.thorn40
London, United Kingdom
graeme.thorn40 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 • 93 views
ADD COMMENTlink modified 12 days ago • written 18 days ago by graeme.thorn40

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 18 days ago by b.nota5.0k

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 12 days ago by graeme.thorn40
1
gravatar for graeme.thorn
12 days ago by
graeme.thorn40
London, United Kingdom
graeme.thorn40 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 12 days ago by graeme.thorn40
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