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Allele equivalency table for SNP60 chip


Juan P. Steibel

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PRRSV
Files with equivalency of alleles in porcine SNP60 chip
Summary
  Researchers sometimes use Forward allele or A/B allele coding, sometimes they are also interested in the actual base in the forward strand of the reference genome.
In our lab we use this equivalency table to go back and forth between diferent "notations'.

Authors: Juan P. Steibel, 
Contributors: Yvonne Badke, Yijian Huang, Jose Luis Gualdron

Contact: steibelj@msu.edu
Download
Equivalency table
Before using this blindly, please read this comment by Bob Schnabel and the explanation on TOP/BOTTOM strand and A/B allele coding
Documentation
Column explanation
References
Badke, Y.M.; Bates, R.O.; Ernst, C.W.; Schwab, C.; Fix, J.; Van Tasell C.V.P. and Steibel, J.P. Methods of tagSNP selection and other variables affecting imputation accuracy in swine. Badke et. BMC Genetics 2013, 14:8

Badke, Y.M.; Bates, R.O.; Ernst, C.W.; Schwab, C. and Steibel, J.P.  Estimation of linkage disequilibrium in four US pig breeds. 2012. BMC Genomics 2012, 13:24.
To-do list
Add table with SNP from chip found in our transcriptome (RNAseq) data
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