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, 17:25, 10 February 2016
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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 uniq - -o dbsnp.normalized.uniq.vcf | | vt normalize dbsnp.vcf -r seq.fa | vt uniq - -o dbsnp.normalized.uniq.vcf |
| + | |
| + | #read in variants that do not contain N in the explicit alleles, normalize variants, send to standard out. |
| + | vt normalize dbsnp.vcf -r seq.fa -f "~VARIANT_CONTAINS_N" |
| | | |
| #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. |