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184 bytes removed
, 15:52, 12 January 2017
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| </div> | | </div> |
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− | === Remove overlap === | + | === Filter overlap === |
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− | 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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− | usage : vt remove_overlap [options] <in.vcf>
| + | <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 filter_overlap in.bcf -w 1 out.bcf |
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− | options : -o output VCF file [-]
| + | todo: option for considering END info tag for detecting overlaps. |
− | -I file containing list of intervals []
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− | -i intervals []
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− | -? displays help
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− |
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− | <div class=" mw-collapsible mw-collapsed">
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− | #removes the INFO tags OLD_VARIANT, ENTROPY, PSCORE and COMP
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− | vt rminfo exact.del.bcf -t OLD_VARIANT,ENTROPY,PSCORE,COMP -o rm.bcf
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| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | usage : vt rminfo [options] <in.vcf>
| + | usage : vt filter_overlap [options] <in.vcf> |
− | | + | |
− | options : -o output VCF file [-]
| + | options : -o output VCF file [-] |
− | -q do not print options and summary [false]
| + | -w window overlap for variants [0] |
− | -t list of info tags to be removed []
| + | -I file containing list of intervals [] |
− | -I file containing list of intervals []
| + | -i intervals [] |
− | -i intervals []
| + | -? displays help |
− | -? displays help
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| </div> | | </div> |
| </div> | | </div> |