IndelLDplot

IndelLDplot: a pipeline mining the 1000 Genomes database to search for functional variations

IndelLDplot is an R- and Perl-based pipeline, mining the 1000 Genomes database to search for functional variations, including indels, with high linkage disequilibrium (LD) values with user-interested SNPs. For easy visualization, genotyping results with high LD variations are conveniently exported to a linkage format viewable by the software Haploview. Those with high LD variations are anno-tated by two individual software, Variant Effect Predictor and ANNOVAR.. The pipeline can be implemented in R cloud or on a local computer running the Ubuntu or Macintosh operating system.