By using snp-sites (https://github.com/sanger-pathogens/snp-sites) I extracted the SNPs with Linux command: snp-sites file name.fasta. This script just extracting the SNPs without position information. I know the genomic positions of my reference sequence. My question is: How to add the genomic position of reference sequence to the aligned fasta sequences as an input to obtain the result of SNPs with genomic positions information as an output. Please let me know an additional script to extract genomic positions of SNPs output from the aligned fasta sequences, besides the SNPs extracting script (snp-sites file name.fasta). Apart from Linux based SNPs extraction, it will be appreciated, If some one knows about R script or R Packages for SNPs genomic positions extraction along with SNPs extraction, please post here. Thanks