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
how to extract the genomic positions and chromosome number for a list of genes