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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.
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#views mills.bcf and outputs to standard out
vt view mills.bcf
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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
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=== Index ===
Indexes a VCF.GZ or BCF file.
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#indexes mills.bcf
vt index mills.bcf
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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
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=== Normalization ===
=== Normalization ===
-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
-- ignores the rest of the labeled arguments following this flag
-h displays help
-h displays help
