SNPs and their neighboring nucleotides

[exo]

Hey,

I was wondering whether anyone out there has a script or a software capable of extracting SNPs with its neighboring bases from read mapping.

What i am interested in is to check for specific mutational signatures where for example a G-->C base substitution and whether this G is preceded by an A, G, C or T and followed by A, G, C or T in the trinucleotide context.

Any help would be appreciated!

[dziq]

Try this http://dziq.pl. You have to download FASTA file of your gene from NCBI. Then enter SNP to text field. Script will show you place where SNP starts.

[exo]

Thank you! But this won't show me the low variants, that are not present in the consensus sequence.
I was looking to track within host evolution and whether that has any unique mutational signatures.