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, 12:11, 5 December 2013
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| You may modify the STDOUT to output the binary version of the format. | | You may modify the STDOUT to output the binary version of the format. |
| | | |
− | == Programs == | + | == VCF Manipulation == |
| + | |
| + | === View === |
| + | |
| + | |
| + | Views a VCF or BCF or VCF.GZ file. Eventually to support filters, subsetting of samples. |
| + | |
| + | <div class=" mw-collapsible mw-collapsed"> |
| + | #views mills.bcf and outputs to standard out |
| + | vt view mills.bcf |
| + | <div class="mw-collapsible-content"> |
| + | usage : vt view [options] <in.vcf> |
| + | |
| + | options : -o output VCF/VCF.GZ/BCF file [-] |
| + | -v variant type [] |
| + | -p print options and summary [] |
| + | -I file containing list of intervals [] |
| + | -i intervals [] |
| + | -- ignores the rest of the labeled arguments following this flag |
| + | -h displays help |
| + | </div> |
| + | </div> |
| + | |
| + | === Index === |
| + | |
| + | |
| + | Indexes a VCF.GZ or BCF file. |
| + | |
| + | <div class=" mw-collapsible mw-collapsed"> |
| + | #indexes mills.bcf |
| + | vt index mills.bcf |
| + | <div class="mw-collapsible-content"> |
| + | usage : vt index [options] <in.vcf> |
| + | |
| + | options : -p print options and summary [] |
| + | -- ignores the rest of the labeled arguments following this flag |
| + | -h displays help |
| + | </div> |
| + | </div> |
| | | |
| === Normalization === | | === Normalization === |
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| -b input BAM file [] | | -b input BAM file [] |
| -i input candidate VCF file [] | | -i input candidate VCF file [] |
− | -- ignores the rest of the labeled arguments following this flag
| |
− | -h displays help
| |
− | </div>
| |
− | </div>
| |
− |
| |
− | === View ===
| |
− |
| |
− |
| |
− | Views a VCF or BCF or VCF.GZ file. Eventually to support filters, subsetting of samples.
| |
− |
| |
− | <div class=" mw-collapsible mw-collapsed">
| |
− | #views mills.bcf and outputs to standard out
| |
− | vt view mills.bcf
| |
− | <div class="mw-collapsible-content">
| |
− | usage : vt view [options] <in.vcf>
| |
− |
| |
− | options : -o output VCF/VCF.GZ/BCF file [-]
| |
− | -v variant type []
| |
− | -p print options and summary []
| |
− | -I file containing list of intervals []
| |
− | -i intervals []
| |
− | -- ignores the rest of the labeled arguments following this flag
| |
− | -h displays help
| |
− | </div>
| |
− | </div>
| |
− |
| |
− | === Index ===
| |
− |
| |
− |
| |
− | Indexes a VCF.GZ or BCF file.
| |
− |
| |
− | <div class=" mw-collapsible mw-collapsed">
| |
− | #indexes mills.bcf
| |
− | vt index mills.bcf
| |
− | <div class="mw-collapsible-content">
| |
− | usage : vt index [options] <in.vcf>
| |
− |
| |
− | options : -p print options and summary []
| |
| -- ignores the rest of the labeled arguments following this flag | | -- ignores the rest of the labeled arguments following this flag |
| -h displays help | | -h displays help |