Question: Indel detectors for Ion Torrent data
gravatar for genya35
14 months ago by
genya350 wrote:


Could someone please suggest a good indel detector to use on IonTorrent BWA-Mem aligned bam files. I've tried Pindel and achieved good results, however, some indels are still missed.


indel • 606 views
ADD COMMENTlink modified 14 months ago by Kevin Blighe33k • written 14 months ago by genya350
  1. Was there a recalibration step with known indels post alignment?
  2. You can also try PINDEL derivatives like DINDEL, GINDEL etc. DINDEL takes output from PINDEL.
ADD REPLYlink written 14 months ago by cpad011210k
gravatar for Kevin Blighe
14 months ago by
Kevin Blighe33k
Republic of Ireland
Kevin Blighe33k wrote:

I think that pindel is fine. The issue may relate to the general issues of calling indels from NGS data.

Some things to consider:

  • Have you visually look at how the reads have aligned over the regions in which indels were not called? They may be problematic regions, like for example homopolymeric regions. I would load your aligned BAMs into IGV
  • Check your mapping quality (MAPQ) filter thresholds (reads with indels will automatically receive lo MAPQ unless we specifically treat them differently
  • Consider your indel length in relation to your read length. As you're using Ion Torrent, I guess that your reads are ~75bp? If you are trying to detect indels from reads of this size, it will always be difficult.
  • Consider downloading your BAMs from the Torrent Server and then using something like GATK IndelRealigner followed by HaplotypeCaller in order to attempt to identify the indels.
ADD COMMENTlink written 14 months ago by Kevin Blighe33k
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