Question: Indel detectors for Ion Torrent data
gravatar for yelekley7
8 months ago by
yelekley70 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 • 420 views
ADD COMMENTlink modified 7 months ago by Kevin Blighe21k • written 8 months ago by yelekley70
  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 7 months ago by cpad01126.3k
gravatar for Kevin Blighe
7 months ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k 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 7 months ago by Kevin Blighe21k
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