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=== Remove overlap ===
=== Filter overlap ===
description : Removes overlapping variants in a VCF file by tagging such variants with the FILTER flag overlap.
description : Tags overlapping variants in a VCF file with the FILTER flag overlap.
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#adds a filter tag "overlap" for overlapping variants within a window size of 1 based on the REF sequence.
vt filter_overlap in.bcf -w 1 out.bcf
todo: option for considering END info tag for detecting overlaps.
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usage : vt filter_overlap [options] <in.vcf>
options : -o output VCF file [-]
-w window overlap for variants [0]
-I file containing list of intervals []
-i intervals []
-? displays help
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