Can SelectVariants be used to limit VCF files by interval list
Posted in Ask the GATK team | Last updated on


Comments (1)

Hello I would like to subset a VCF file to only save a few specific regions of the whole genome. I know some of your tools allow for an interval list to be used to subset the region analyzed. Do you have a tool or are you aware of a tool that would allow me to quickly do this from an interval list or something similar? I could make a little script myself, but I figure sub setting and printing out a specific genomic region of interest in a VCF file has to be a solved problem by GATK.

Thanks for your help! ~Sean


Return to top Comment on this article in the forum