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?
You're probably going to want to get very familiar with bedtools: http://bedtools.readthedocs.org/en/latest/
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.
create a BED file containing the CpG sites and then filter your vcf file with tools like bedtools intesect
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?
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
Log in to answer this question.
Identifying CpG islands given a vcf variant file
Thank you :) I will read this.