how to generate CIGAR like string?

Question

[crivenster]

Hi, I have two sequences and I would like to generate indels for them. As the alignment just gives the score, to represent the the alignment of the two sequence I would like to generate CIGAR .

[iraun]

Just open the sequences with a text editor and insert/delete some bases? Maybe I'm missing something in your question...

[crivenster]

Yes. I got confused with indel and cigar string. Just updated the question.

Answer 1

[Devon Ryan]

1. Use a random number generator to pick a position
2. Use a random number generator to pick an InDel length
3. Using the above, add (possibly random) sequence of the given length at the given position
4. ?
5. profit

Alternatively, just add some in manually if you just have two sequences and you don't need many indels. You can just randomly pick some positions.

[crivenster]

I just updated the question. I had confused with indel and cigar string.i want to generate cigar string so that it explains alignment information better.

[Devon Ryan]

So in other words, you want to align two sequences and get the resulting CIGAR string? Are you aligning them manually or with a program. In the latter case, just use a program that will generate CIGAR strings. In the former case, you can just generate one yourself (CIGAR strings aren't exactly complicated things).

[crivenster]

I align them using local alignment programs. Is there any program that just generates CIGAR? Generating CIGAR for small sequences is simple,but larger ones takes time.

[Pierre Lindenbaum]

answer Devon's questions please.

[Devon Ryan]

Then use a local alignment program that will produce a CIGAR string (or at least something that you can then convert into one). Alternatively, if the programs output a formatted pairwise alignment, then just parse that (the only hard parts are the ends, which can be soft-clipped).