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184 bytes removed, 15:52, 12 January 2017
Remove overlap
=== Remove Filter overlap ===
description : Removes Tags overlapping variants in a VCF file by tagging such variants with the FILTER flag overlap.
usage : <div class=" mw-collapsible mw-collapsed"> #adds a filter tag "overlap" for overlapping variants within a window size of 1 based on the REF sequence. vt remove_overlap [options] <filter_overlap in.vcf>bcf -w 1 out.bcf
options todo: -o output VCF file [-] -I file containing list of intervals [] -i intervals [] -? displays help <div class=" mw-collapsible mw-collapsed"> #removes the INFO tags OLD_VARIANT, ENTROPY, PSCORE and COMP vt rminfo exact.del.bcf -t OLD_VARIANT,ENTROPY,PSCORE,COMP -o rmoption for considering END info tag for detecting overlaps.bcf
<div class="mw-collapsible-content">
usage : vt rminfo filter_overlap [options] <in.vcf> options : -o output VCF file [-] -q w do not print options and summary [false] -t list of info tags to be removed window overlap for variants [0] -I file containing list of intervals [] -i intervals [] -? displays help

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