Question: CpG-SNPs for newbies
0
gravatar for Svetlana Frenkel
19 months ago by
Israel / University of Haifa
Svetlana Frenkel0 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 • 735 views
ADD COMMENTlink modified 19 months ago by Pierre Lindenbaum101k • written 19 months ago by Svetlana Frenkel0

Identifying CpG islands given a vcf variant file

ADD REPLYlink written 19 months ago by venu4.5k

Thank you :) I will read this.

ADD REPLYlink written 19 months ago by Svetlana Frenkel0
2
gravatar for Daniel Swan
19 months 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 19 months 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 19 months ago by Svetlana Frenkel0
1
gravatar for Pierre Lindenbaum
19 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum101k wrote:

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

ADD COMMENTlink modified 19 months ago • written 19 months ago by Pierre Lindenbaum101k

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 19 months ago by Svetlana Frenkel0
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