Fast way to get 0-distance, 1-distance, or x-distance reads aligned to reference

Question

[chongchu.cs]

Given short reads and reference, I wonder is there a way or tool can quickly find out which reads are x-distance (x can be 0,1,2,...hamming distance from the reference) aligned to the reference?

Thank you.

Answer 1

[Brian Bushnell]

I think Bowtie1 can do that, up to a hamming distance of 3. I'm not certain whether Bowtie1 guarantees finding all possible sites for hamming distance 0-3, but it might.

BBMap can do that fairly accurately for a pretty high hamming distance (perhaps 10% of the read length), if you use the flag strictmaxindel=0. But, it will not guarantee correctness in cases where a read maps better with an indel than with tons of substitutions; instead, it will map the read with an indel and then discard it because it fails your filter of having indels.