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  • Extract neighbourhood bases of a SNP

    I have downloaded the COSMIC mutation data (.maf file). Now for each mutation, I want to extract one base to the left and right of all SNPs. How can I do that? If I download the hg38 reference genome, can I use the variant position to extract bases to the left and right of the mutation? Will that take into account the within-sample variation that each cancer sample might have had?

  • #2
    Hello bong28,

    are you banerjeeshayantan? There is a very similar question on biostars.

    fin swimmer

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