Hi I'm working on Sanger sequencing reads to detect the variants and annotate them, i have only one Sanger read from specific regions (exon in example) of the genome of the patient, using sangerseqR package in R to work with it. in some patients sanger data, one of the two copies of the region have some indel so bases shift and signal start to have two peaks. along with some mismatches how to fix the data and find indel variants?
from Mom: A C G T A C G T from Dad: A C G - A C G T
so the sanger will report:
and from the 4th base there will be two peaks and basecaller may report this instead:
any idea to solve this? is there any package or function to handle that? any software who report indels? thanks all