Find occurrence of short pattern in fasta with several sequences and ouput it to bam

Question

[mschmid]

I have a 20 nucleotide pattern. Now I want to find ALL of its occurences in a fasta file with about 200 sequences.

Then I want to ouput the positions either to a gff or into a sam file to be able to load into IGV. What is the most efficient way to do that?

It can have about 1-2 indels and about 2-4 SNPs. It is just important to find where the approximate pattern occurs often...

Answer 1

[Sean Davis]

How about good old blat or gmap?