SNPlotz: a generic genome plot tool to aid the SNP association studies
KeywordsPhenotypic Association Equivalent Program Graphic Capability Causal Candidate Important Quantitative Trait
High throughput SNP genotyping has empowered livestock researchers to perform genome wide association studies to discover genes responsible for complex traits or economically important quantitative traits. The analysis of large numbers of genotypes is not only a challenge for statistical data analysis but also presents a tedious job for users to interpret and comprehend the large number of statistics generated. A simple and fast approach is to plot the phenotypic association values of each SNP against their genome locations. The benefit is twofold: (1) certain genome locations may quickly draw attention if many closely located SNPs are found to show higher degree of associations to traits. (2) It is feasible to locate causal candidate genes when the genome plot is aligned with genomic features such as transcripts, genes, or mapped QTL.
Materials and methods
This article is published under license to BioMed Central Ltd.