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319 bytes added, 12:41, 2 July 2015
[ Normalize] variants in a [ VCF] file [ (Tan et al. 2015)] . 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 which may be changed via the -w option. There is an underlying assumption that the REFfield is consistent with the reference sequence use, vt will check for this and will fail if reference inconsistency is encountered; this may be relaexd with the -n option.
-d debug [false]
-q do not print options and summary [false]
-n do not fail when REF is inconsistent with reference sequence for non SNPs [false]
-w window size for local sorting of variants [10000]
-I file containing list of intervals []

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