Hi,

I have a list of fastq files on which I am trying to run a (suitable) variant calling pipeline. The question here is to do variant calls on the data and then compare it with a list of genes of interest. I would like to extract the genomic coordinates or other gene information that could minimize computational work load as I will be working on the server with limited space (And want to save time as well).

I have both gene names and ENS IDs that I can use to find their coordinates which can help me in understanding the results from variant call file (vcf file). Can anyone please suggest any R packages or other tools that I can use to fetch genomic coordinates?

For instance, if all of the disease causing genes are present in only a few chromosomes, then I will not have to keep other chromosomes while running my VCF pipeline (from making alignments to calling variants).

Best regards, Salman