Sequence extraction chromosome wise

Question

[bioinfo456]

I have a vcf file containing the location of certain SNPs. I want to know if there exists an R package that outputs nucleotide sequence 1000 bp up and downstream of the given SNP location. Thanks in advance.

[Pierre Lindenbaum]

similar questions have been asked before. Please search this site.

Answer 1

[zx8754]

Hello Uday Rangaswamy!

Questions similar to yours can already be found at:

• Get Flanking Sequence Given A List Of Positions
• Extract Flanking Region Of A Snp
• pull out flanking sequences of snp
• extract sequence around snp
• Extract surrounding genome sequences given certain locations using R

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