![]() The Sort Variant By options allow you to sort the set by a trait of a specific variant. To change the color coding of the plot, select Color By>Allele. To change this, right-click and select Set Feature Visibility Window. The window size at which VCF data is loaded is proportional to the number of samples. Find more details on the menu options on the Pop-up Menu page. Some of the options are specific to the variant selected. To see the options for changing the view of your VCF file, right-click on a variant. If a file has more than 10 genotypes, the VCF file will be opened in its own pane, with a scroll bar, as shown below. Dark blue = heterozygous, Cyan = homozygous variant, Grey = reference. The genotypes for each locus in each sample. VCF calls are available at EBI / NCBI.Įach bar across the top of the plot shows the allele fraction for a single locus. ![]() The format is further described on the 1000 Genomes project Web site. VCF stands for Variant Call Format, and this file format is used by the 1000 Genomes project to encode SNPs and other structural genetic variants.
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