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Old 05-21-2018, 08:17 AM   #1
bong28
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Location: India

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Default 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?
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Old 05-24-2018, 08:39 PM   #2
finswimmer
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Hello bong28,

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

fin swimmer
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next-gen seq, snp analysis, vcf analysis tools

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