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, 13:41, 2 July 2015
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| <div> | | <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 [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 | | [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. | + | 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 REF |
| + | field 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. |
| </div> | | </div> |
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| -d debug [false] | | -d debug [false] |
| -q do not print options and summary [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] | | -w window size for local sorting of variants [10000] |
| -I file containing list of intervals [] | | -I file containing list of intervals [] |