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530 bytes added
, 20:09, 9 June 2020
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| </div> | | </div> |
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− | === Remove overlap === | + | === Filter overlap === |
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| 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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− | <div class=" mw-collapsible mw-collapsed"> | + | <div class="mw-collapsible mw-collapsed"> |
| #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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| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | usage : vt remove_overlap [options] <in.vcf> | + | usage : vt filter_overlap [options] <in.vcf> |
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| 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 |
| + | </div> |
| + | </div> |
| + | |
| + | <div class="mw-collapsible mw-collapsed"> |
| + | #Use Remove overlap instead for versions older than Jan 12, 2017 |
| + | vt remove_overlap in.vcf -r hs37d5.fa -o overlapped.tagged..vcf |
| + | |
| + | <div class="mw-collapsible-content"> |
| + | 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 |
| </div> | | </div> |
| </div> | | </div> |