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, 16:34, 12 January 2017
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| -? displays help | | -? displays help |
| </div> | | </div> |
| + | </div> |
| + | |
| + | === Filter === |
| + | |
| + | Filters variants in a VCF file |
| + | |
| + | <div class=" mw-collapsible mw-collapsed"> |
| + | #adds a filter tag "refA" for variants where the REF column is a A sequence. |
| + | vt filter in.bcf -f "REF=='A'" -d "refA" |
| + | |
| + | <div class="mw-collapsible-content"> |
| + | usage : vt filter [options] <in.vcf> |
| + | |
| + | options : -x clear filter [false] |
| + | -f filter expression [] |
| + | -d filter tag description [] |
| + | -t filter tag [] |
| + | -o output VCF file [-] |
| + | -I file containing list of intervals [] |
| + | -i intervals |
| + | -? displays help </div> |
| </div> | | </div> |
| | | |
| === Filter overlap === | | === Filter overlap === |
| | | |
− | description : Tags overlapping variants in a VCF file with the FILTER flag overlap.
| + | Tags overlapping variants in a VCF file with the FILTER flag overlap. |
| | | |
| <div class=" mw-collapsible mw-collapsed"> | | <div class=" mw-collapsible mw-collapsed"> |