I would like to learn how to convert the genome positions (e.g., Chr6: 467841) into other useful identifiers and annotations. For example, I use the vcftools to get only SNPs in a ".012" format, which also outputs the site locations (i.e., genome positions) in a ".012.pos" file. I use the following command:
vcftools --vcf xxx.vcf --out SNP --remove-indels --012
Basically, it creates "SNP.012" that only contain 0,1,2 values and "SNP.012.pos" that contains the site location like:
Chr1 2673 Chr1 2695 Chr1 2696
I would like to match these site locations (i.e., genome positions) to variant identifiers to genome annotations. I have some success in loading a gff3 file (e.g., NCBI genome annotation downloaded) and doing left/right joins in R. But it seems somewhat ad hoc. I tried to use Bioconductor packages (GenomicRanges, GenomicFeatures, biomaRt) but I couldn't find efficient/fast/best practices. FYI, I prefer working in R/Bioconductor.