Gene variation study through blast tab limited out put

Question

[Eva_Maria]

I took a gene and aligned into 300 genome using Blast. From this Blast output (tab limited) how can I find gene variations(SNPs). Please help me

[Ram]

Using BLAST to call SNPs is not a great idea. BLAST is a local aligner, AFAIK not a tool designed to work with the probabilistic algorithms used to call variants.

The protocol would involve a LOT of manual work, where you'd have to look for matches covering all of the query, with as few mismatches as possible, then examine each mismatch to identify what kind of variant it is, all the while never losing sight of the bigger picture. And because this involves carefully eyeballing each sequence, tab-delimited output will not work for you.

You may want to look up possible alternatives to this protocol.