Hi all. Thus far, have figured out how to convert a large .SRA file that was obtained from the NCBI to fastq format--but I have the SRA Toolkit downloaded on my Mac, so according to what I've found online so far, I think that I could just as easily convert this file to ABI SOLiD native, fasta, sff, sam, or Illumina native using similar commands in the Mac Terminal.
My question: what is the best program/approach to go from .SRA data to being able to search for specific SNPs by their rs number? Is Illumina's Genome Studio a useful program? Are there other programs/approaches that would be better?