I am attempting to use VCFtools to calculate snp densities of specific genes within a VCF from the Exac Browser. Here is the script that I am using:
vcftools --vcf ExAC.r0.3.1.sites.vep.vcf --chr chromosome_# --from-bp start_coordinate --to-bp end_coordinate --SNPdensity gene_size --out gene_name
--SNPdensity should take the positions I give it, and calculate the SNP density from the gene_size I give it, but my output files are inconsistent. VCFtools seems to be calculating the SNP density but not for the entire region I give it, and I end up with two different SNP densities for outputs.
Has anyone had this issue and figured out how to fix it?