I am having sort of a non-conform problem.
we have a mutated mitochondrial genome (circular) of high coverage (~x10k). We know that there are a few deletions and insertions in there due to genomic re-organizations, breakdown and re-alignments. We have the mutated line and a wild-type line. we would like to compare both lines in the number of indels
Problem: As mitochondria have different genomes in one cell, not all of the mitochondria will have these deletions. We also estimate the number of reads which can show these deletions to be relatively low. We expect so see big deletions (5-8Kb in size)
proposed solutions: I ran tophat to look for junctions. The junctions will mark splitted reads which were mapped at both ends of the deletion. We also found some very large deletions, but only in very few reads (1-3).
I was wondering if there any tools out there who can confirm such results or maybe do a better indel analysis on low number of reads.
(I already tried Pindel and it couldn't show me the correct deletions, probably due to the fact that there were not enough reads)
Thanks for any help or ideas.