How to identify snps in gene


I'm trying to identify snp in a gene. But when I was looking for information about it / software for snp calling, mostly the ones I saw involve snp in genome sequence instead of only involving a specific gene. So can someone give some advice on how can I identify snp of a gene?




To expand on the comment by Ram first and foremost the type of data that you have determines the process by which you can establish a SNP.

If you have genome-wide high throughput data, then your methods will have to be genome-wide alignment, then variant-calling followed by identifying the coding regions of the gene of interest and then looking for SNPs in those regions.

If you have single long sequences specific to one gene, then you would perform a pairwise alignment between your data and the reference, then use the results of that to directly identify mismatching bases as SNPs.

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