I need some help getting started on this project.
To simplify we want to be able to quantify the occurrence of 3 variants on each sequencing read in an alignment file as a proxy measurement for recombination.
The possible combinations we have are A, B or AB.
For example, variant A is at position 100 and variant B is at position 300 of the reference and AB would have both.
We have alignment files against a reference sequence, and then I get stuck. I could technically look by eye in tablet or IGV for example but is there a way to extract each read then query by expected base at the reference position then bin these reads into the categories; A, B, AB and unclassified then calculate the total occurrences of each?
Thanks for your time and suggestions!