Defining haplotypes in genic and non-genic regions using user specified window size

Haplotype analysis divulges more information in correlating genotype to phenotype compared to individual SNP based analysis. In this regard an in-house Perl based tool has been developed to identify the haplotypes from the SNP genotyping data in genic and non-genic regions of the chromosome based on a user specified window size. The tool works in three stages. First the tool identifies the genic (including exon, intron, 3’ and 5’ UTR) and non-genic regions of the chromosome based on the genome annotation. Non-genic regions are divided into user specified window sizes starting from the 5’ end of the gene and the 3’ end of the adjacent gene towards the centre of the intergenic region in both directions. A similar strategy is applied towards telomeric ends. Finally haplotypes are defined from the genic and non-genic regions. The SNP genotyping information and the haplotypes are visualized in a genome browser (GBrowse) as tracks, which allow users to inspect the specific regions of the genome in which they may be interested. GBS data on the reference set of sorghum (371 diverse germplasm lines) consisting of ~556K SNPs is used for identifying haplotypes. The non-genic regions of the chromosomes are divided into 5kb windows. An average of 4806 windows are identified per chromosome with 12 haplotypes per window from a total of 175425 called SNPs (after filtering for minor allele frequency (MAF) (20%) and imputation of the missing data using the NPUTE program) across the genome. These haplotypes are now being utilized for downstream analysis such as GWAS. This tool is available for the users to download and the tool can be utilised to identify genic and non-genic haplotypes in any organism which has annotation and SNP genotyping information.