Selecting all variants that overlap a specific position
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Hi,

I have a vcf file of indels, and an interval file of single-base positions I am interested in. I would like to select all of the variants in the file that overlap the positions I'm looking at. Using select variants with the interval list I have returns nothing, because the indels are not contained within any intervals. I don't want to just add an arbitrary amount of padding to my intervals because I don't want to include other nearby variants that don't actually overlap my sites.

Is there a way to do this easily in GATK?


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