CpG-SNPs for newbies

Question

[Svetlana Frenkel]

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?

[venu]

Identifying CpG islands given a vcf variant file

[Svetlana Frenkel]

Thank you :) I will read this.

Answer 1

[User 59]

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

[Svetlana Frenkel]

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.

Answer 2

[Pierre Lindenbaum]

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

[Svetlana Frenkel]

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?

[Shicheng Guo]

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