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title: "Extract VCFs"
canonical: "https://help.biobam.com/space/OUM3/3675852631/Extract%20VCFs"
format: markdown
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Introduction Sometimes, although you have a huge whole-genome VCF file with a lot of samples, you just want to analyze only some samples or you want to focus on some chromosomes of the genome. Because of that, we have added a tool to extract features from a VCF to OmicsBox. Extract VCF The tool to extract features from a VCF can be found in the Genetic Variation Module of OmicsBox under  VCF Tools → Extract from VCF.  The wizard consists of two pages and allows you to define the input and output options as well as different options to extract information from VCF files ( Figure 1 ,  Figure 2 ). Input In the first page you will be able to select the input file and what information you want to extract. VCF File:  select the VCF file from which to extract information. Features to extract by: Samples:  choose this option if you intend to generate a VCF file with the same number of variants as the original one but with only certain samples. Chromosomes:  select this option if you want to create a VCF file with all the samples as the original file but with variants from selected chromosomes.  Features to extract:  select the samples/chromosomes that you want to extract. Get Also Unselected Features:  select this option if you want to obtain not only a VCF file with the selected features but also another one with the opposite subset of features. The last option might be interesting in the case that you have a lot of chromosomes/samples and you want to extract the majority of them. As selecting all of them might be a bit arduous, you can select the features you are not interested in and then check this option.  Figure 1.  Input  Page Output VCF File:  specify where to save the VCF file with the extracted features. Complementary VCF File:  specify where to save the VCF file with the complementary set of features. Figure 2.  Output Page Summary Report Appart from the VCF file(s), a Summary Report will appear. This report will have the following information: Input Data:  file names of all the VCF used as input. Summary Information: Types of Variants: frequency of the different types of variants. Number of alleles in a variant: abundance of the alleles per variant. Statistics: number of total variants, number of total genotypes, number of heterozygotes and missing data. Figure 3.  Summary Report