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Three allele calls for a diploid organism
Not sure what to make of this one-- I have a diploid fish that I'm examining an interesting variant for. I generated a "bamout" file using Haplotype caller for one particular individual to examine the raw reads.
Strangely, there are at least three distinct variants present in the reads for this fish! There is either an A/G or deletion at this site. This leads haplotype caller to produces a VCF that calls an INDEL on top of the SNV (A/G), which is what motivated me to initially inspect this file. The flanking SNVs (and the vast majority of sites) are biallelic), and I have no reason to suspect my fish is triploid. Is this something artefactual produced by the strange structural variation in this location? Any parameter tweaks that folks can suggest that make this start to make sense?
In attatchment are the Artificial Haplotype read groups produced by HaplotypeCaller, and a second attatchment shows the actual reads supporting this mess. Any help would be greatly appreciated!!