I have a short sequence, which has been mapped to the genome with known numbers of mismatches and INDELs. Below shows an example:
target sequence: ATGGATCGTACGTAACGCTAGCATGACT, query sequence: ATGCGTCCGCGTAACG, mismatch No.: 6, INDEL No.: 3.
based on the above information, how to generate the following pattern, in other words, how to output the mismatch and INDEL position information?
ATG-GATCGTACGTAACGCTAGCATGACT ||| | || || ||| ATGCG-TCCGCG-TAACG
Thank you very much.