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Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Can SelectVariants be used to limit VCF files by interval list

sboylesboyle Bay Area, CAPosts: 28

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

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