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#normalize variants, send to standard out and remove duplicates.
#normalize variants, send to standard out and remove duplicates.
vt normalize dbsnp.vcf -r seq.fa | vt mergedups - -o dbsnp.normalized.merged.vcf
vt normalize dbsnp.vcf -r seq.fa | vt mergedups - -o dbsnp.normalized.merged.vcf
#variants that are normalized will be annotated with an OLD_VARIANT info tag.
#CHROM POS ID REF ALT QUAL FILTER INFO
19 29238772 . C G . PASS VT=SNP;OLD_VARIANT=19:29238771:TC/TG
20 60674709 . GCCCAGCCCCAC G . PASS VT=INDEL;OLD_VARIANT=20:60674718:CACCCCAGCCCC/C
#this shows a sample output with the normalization operations that were used
#categorized into 5 categories each for biallelic and multiallelic variants. <br>
stats: biallelic
no. left trimmed : 156908
no. right trimmed : 323
no. left and right trimmed : 33
no. right trimmed and left aligned : 7
no. left aligned : 12360 <br>
total no. biallelic normalized : 169631 <br> <br>
multiallelic
no. left trimmed : 627189
no. right trimmed : 2509
no. left and right trimmed : 1498
no. right trimmed and left aligned : 212
no. left aligned : 1783 <br>
total no. multiallelic normalized : 633191 <br>
total no. variants normalized : 802822
total no. variants observed : 88052639
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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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=== Decompose===
<div>
[http://genome.sph.umich.edu/wiki/Variant_Normalization Normalize] variants in a [http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42 VCF] file. Normalized variants may have their positions changed; in such cases, the normalized variants
are reordered and output in an ordered fashion. The local reordering takes place over a window
of 10000 base pairs.
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#decomposes multiallelic variants into biallelic variants and write out to gatk.decomposed.vcf
vt decompose gatk.vcf -o gatk.decomposed.vcf
#variants that are normalized will be annotated with an OLD_VARIANT info tag.
#variants that are normalized will be annotated with an OLD_VARIANT info tag.
