Searching bases in reference genome.

[kasthuri]

Is there a command line tool that would give me the nucleotide before and after a given mutation/variant base?

Thanks
-Kasthuri

[qtrinh]

You can use samtools to do this. i.e., samtools faidx REGION

[kasthuri]

Great! Thanks. Well, for example, it is samtools faidx filename.fasta chr1:139266-139268 (to make it easy for folks who may have this question in future). Reference fasta should be indexed first using samtools faidx.


-Kasthuri