IndelLDplot

IndelLDplot is a pipeline written in SAS statistical language, mining the 1000 Genomes database to search for functional variants, including indels, with high linkage disequilibrium (LD) values to user-interested single nucleotide polymorphisms (SNPs). IndelLDplot can annotate these high LD variants with ANNOVAR. In addition, IndelLDplot can map these variants to Ensembl Regulatory Regions. Furthermore, IndelDplot can carry out cis-acting expression quantitative trait loci (cis-eQTL) analysis with genome-wide expression dataset as well as the corresponding next generation sequencing dense genotyping of lymphoblastoid cell lines (LCLs) provided by the 1000 Genomes Project among 432 individuals across six population groups.