Hey everyone
I would like to make a description of the genes affected by SNPs.
I have a long list of the locations of SNPs in my reference genome. I have my Prokka output, so i have the annotated genome. I could just go and search for each single snp location and write down the gene the SNP is located in. However i have thousands of SNPs so i need to have a tool to do this for me. Does anyone have knowledge of af software like that.
thanks
Hi Steffen, you could try SnpEff, a Genetic variant annotation and effect prediction toolbox @ http://snpeff.sourceforge.net/
This is my go to tool for annotation of SNPs in a mapped reference genome (in vcf format)
Well i already have the reference annotated, i just want to have a list of genes in which there are snps.
Hi Steffen,
As mentioned by Daniel, SnpEff is the best tool for your requirement. Look at this link: http://snpeff.sourceforge.net/SnpEff_manual.html#run
In brief what it does is, it takes an annotated genome as a reference and list of your snps(in vcf format which contains information like position and chromosome of SNP, ID of SNP, reference and alternate nucleotide and some other informations). Based on position in your vcf file, details of corresponding positions in reference genomes is appended in vcf file. So, as a ouput you get a vcf file with added information like region of variant, impact of variant, gene name, gene id, coding/non-coding, cDNA & protein position and changes, etc.
So, basically it can be used to fulfill your purpose. However, since you have mentioned that you have a list of SNPs, you may need to create VCF file based on that.
Hope it helps
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Software