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Vt

319 bytes added, 12:41, 2 July 2015
Normalization
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[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 [http://bioinformatics.oxfordjournals.org/content/early/2015/03/22/bioinformatics.btv112 (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.
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-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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