1,102
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Normalization
<div class=" mw-collapsible mw-collapsed">
<div class=" mw-collapsible mw-collapsed">
#normalize variants and write out to mills.normalized.vcf
#normalize variants and write out to dbsnp.normalized.vcf
vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf
vt normalize mdbsnp.vcf -r seq.fa -o dbsnp.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 | vt mergedups - -o mills.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.
#variants that are normalized will be annotated with an OLD_VARIANT info tag.
#categorized into 5 categories each for biallelic and multiallelic variants. <br>
#categorized into 5 categories each for biallelic and multiallelic variants. <br>
stats: biallelic
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
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
