SNPchiMp v.2: A multi-species database

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What is SNPchiMp?

SNPchiMp v.2 is a free web-based tool that allows researchers to “jump” between different SNP chips and types of information in many species, in an intuitive and user friendly way.
With SNPchiMp v.2 you can, with a few clicks:
  • Know which SNPs are contained in all (or part of) commercial SNP chips currently available for the species considered (e.g. for imputation or data integration);
  • Get chromosome and physical position of your SNPs, updated to the any genome assembly you like.
  • Have your commercial SNP/probe names linked to a [rs/ss]IDs.
  • Have complete access to sender original information, including orientation, strand, etc. (e.g. for integration of your data with full sequence).
  • Obtain direct access to Illumina’s FORWARD/REVERSE or TOP/BOT allele coding customized to the desired SNP chip(s).
  • Obtain the latest version of the Interbull SNP exchange index.
  • Browse your genomic analyses results: explore your results directly, link your SNPs to dbSNP and ENSEMBL.

How to use SNPchiMp?

Why using SNPchiMp?

  • Because there are two main SNPchip producers and many custom SNP chips available that have different output data options.
  • Because higher density SNP chips do not contain all the SNPs in the lower density chips.
  • Because some SNPs have been referenced with different SNP names within the same community.
  • Because there are and there will be updates in the reference assembly, especially for species with a recent reference genome!
  • Because it is hard to find the links between commertial SNP names and rsIDs (that are often searchable terms in all public DBs).
  • Because SNP alleles in output files are difficult to handle (e.g. A/B, FORWARD, TOP)
  • Because for some downstream analyses, knowing the strand of the SNPs (with respect to the reference genome) can be fundamental.

Read more

https://bioinformatics.tecnoparco.org/SNPchimp/

SNPchiMp v.2 is a free web-based tool that allows researchers to “jump” between different SNP chips and types of information in many species, in an intuitive and user friendly way.