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  • SNPs and their neighboring nucleotides

    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!

  • #2
    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.

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    • #3
      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.

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