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vt normalize <input.vcf> -r <sequence.fa> -o <output.vcf>
vt normalize mills.vcf -r seq.fa -o - mills.normalized.vcf
#normalize variants, send to standard out and remove duplicates.
#normalize variants, send to standard out and remove duplicates.
vt normalize mills.vcf -r seq.fa -o - | vt merge_duplicate_variants - -o mills.normalized_merged.vcf
vt normalize mills.vcf -r seq.fa -o - | vt merge_duplicate_variants - -o mills.normalized_merged.vcf
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usage : vt normalize [options] <in.vcf>
options : -o output VCF file [-]
-I file containing list of intervals []
-i intervals []
-r reference sequence fasta file []
-- ignores the rest of the labeled arguments following this flag
-h displays help
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