A number of SNPs appear to be associated with a trait of interest. I wish to look into all of these SNPs and get an idea of how they affect genes and whether they correspond to insertions or deletion mutations (indels).
I do not have access to genome sequence data for the GWAS population, only SNP files (28M SNPs for ~900 individuals with ~350Mb genome), which I have in a number of formats including .bed, .ped, .tped, and .vcf. The available dataset only includes the SNP identity, which is A, G, C, T or missing. This is from high-coverage genome data and missing SNPs presumably correspond to indels.
Given the information in these files, is there a way for me to find out if SNPs correspond to indels or point mutations? I could just identify SNPs that are missing in some genotypes and assume there's an indel at each specific marker position, but I hope to actually be able to figure out how long the indel is and where it starts and stops, and to do this on a high-throughput scale automatically for hundreds of SNPs.
Is there an existing GUI, command line or R interface for determining if SNPs correspond to indels, or better yet, reconstructing genomes from SNP files so that I can align different alleles and see clearly how SNPs can correspond to indels?
Edit: This is for a non-model plant organism.
Edit 2: Please find below a sample of my .vcf