From Genome Analysis Wiki
Jump to navigationJump to search
28 bytes removed
, 15:09, 2 July 2015
Line 259: |
Line 259: |
| | | |
| <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/31/13/2202 (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 REF | | 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. | | 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. |