<p>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.</p>

<p>The files themselves need reanalysing from the initial FASTQ -> BAM with the newest version.</p>

CC BY-SA 4.0
2018-10-11T11:12:25.207Z
2018-10-11T11:12:25.207Z
user36196
<p>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.</p>

<p>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.</p>

<p>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? </p>

<variant-calling>
IonTorrent variant caller failing, lack of ZM: tags in BAM files
# IonTorrent variant caller failing, lack of ZM: tags in BAM files

(Asked by: username_0 on 2018-10-04)

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?

**Tags:** variant-calling

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## 1 answers

### Answer by username_0 on 2018-10-11. Score: 1 | Accepted 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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