Question: CpG-SNPs for newbies
0
gravatar for Svetlana Frenkel
2.2 years ago by
Israel / University of Haifa
Svetlana Frenkel10 wrote:

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?

cpg snp • 1.0k views
ADD COMMENTlink modified 2.2 years ago by Pierre Lindenbaum108k • written 2.2 years ago by Svetlana Frenkel10

Identifying CpG islands given a vcf variant file

ADD REPLYlink written 2.2 years ago by venu5.3k

Thank you :) I will read this.

ADD REPLYlink written 2.2 years ago by Svetlana Frenkel10
2
gravatar for Daniel Swan
2.2 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

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

ADD COMMENTlink written 2.2 years ago by Daniel Swan13k

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.

ADD REPLYlink written 2.2 years ago by Svetlana Frenkel10
1
gravatar for Pierre Lindenbaum
2.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum108k wrote:

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

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Pierre Lindenbaum108k
1

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?

ADD REPLYlink written 2.2 years ago by Svetlana Frenkel10

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

ADD REPLYlink written 11 hours ago by Shicheng Guo4.9k
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