Align long nucleotide repeats with deletion

Hello, I have a case in which I have a reference sequence that looks as such (5 times 'A') -

TAAAAAT

I have a read that has only 4 A's:

TAAAAT

Is it possible to specify to an aligner where I want the deletion to occur?

For example, can I control between the cases of:

T-AAAAT OR TAAAA-T

Thank you very much for the assistance

repeats deletion alignment

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updated 4.0 years ago by GenoMax 16K • | written 4.0 years ago by Guy 1

You can always edit the alignment manually but I doubt it is possible to control this automatically.

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written 4.0 years ago by GenoMax 16K

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