CpG-SNPs for newbies
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5.2 years ago

Hi I am very new in bioinformatics and I apologize for the stupid questions. But I have almost written my own tool for processing VCF and then found VCFTools, which makes everything faster and better. Now I want to find appropriate tool BEFORE invent my own "bicycle".

I want to detect which SNPs in my VCF located in CpG sites. Any suggestions?

SNP CpG • 2.1k views
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Thank you :) I will read this.

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5.2 years ago
User 59 13k

You're probably going to want to get very familiar with bedtools: http://bedtools.readthedocs.org/en/latest/

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Thank you Daniel. I will read.
As I said to Pierre, I have an idea how to check whether SNP removes CpG site, but some SNPs (with C or G as alt allele) can create new CpG, and in order to find these new CpG I have to detect nearest nucleotide in sequence. And this is problematic, at least right now.

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5.2 years ago

create a BED file containing the CpG sites and then filter your vcf file with tools like bedtools intesect

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Thank you. This helps to check whether SNP removes CpG site, but some SNPs (with C or G as alt allele) can create new CpG. And in order to find these new CpG I have to detect nearest nucleotide in sequence. Do you know any tool for fast navigation in FASTA?

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check the nucleotide after SNPs with 'C' and the nucleotide before SNPs with 'G', then you can identify all these CpG-SNPs. Later I will do the genome-wide analysis and provide a full list of CpG-SNP

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