Hi,

For a given sample, I want to type the G gene of the HLA domain of which I already know the alleles A1, A2, A3, A4, A5, A6 and Ay. After sequencing, I had the following data described in the table. As we can see, the reads R3 and R7 are similar, which means that they align on the same alleles (A4 to Ay). My question is, can I suggest that these 2 reads are duplicates and delete one of them, or should I keep both reads (by suggesting that they are not duplicate and that they align to two different alleles with similar sequence)? Same question for A1 and A2, as we can see that every read that aligns on A2 aligns also on A1?

Thank you, I hope that my question is clear.