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=== Remove overlap ===
=== Filter overlap ===
Removes overlapping variants in a VCF file by tagging such variants with the FILTER flag overlap.
Removes overlapping variants in a VCF file by tagging such variants with the FILTER flag overlap.
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#annotates variants that are overlapping
#annotates variants that are overlapping
vt remove_overlap in.vcf -r hs37d5.fa -o overlapped.tagged..vcf
vt filter_overlap in.vcf -r hs37d5.fa -o overlapped.tagged..vcf
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usage : vt remove_overlap [options] <in.vcf>
usage : vt filter_overlap [options] <in.vcf>
options : -o output VCF file [-]
options : -o output VCF file [-]
-w window overlap for variants [0]
-I file containing list of intervals []
-I file containing list of intervals []
-i intervals []
-i intervals []
-? displays help
-? displays help
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#Use Remove overlap instead for versions older than Jan 12, 2017
vt remove_overlap in.vcf -r hs37d5.fa -o overlapped.tagged..vcf
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usage: vt remove_overlap [options] <in.vcf>
The old version has the same options except that it lacks the -w option
The change occurred in the following commit:
https://github.com/atks/vt/commit/ab5cf7e91b3baa5349f439e6fe92491ae19da1a6
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