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1 CircosVCF: CircosVCF is a web based visualization tool of genome-wide variant data described in VCF files using circos plots. The provided visualization capabilities, gives a broad overview of the genomic relationship between genomes, as well as allowing focusing on specific SNP regions. The user friendly interface of CircosVCF supports for an interactive design of the circles in the plot, as well as integration of additional information such as experimental data or annotations. How To Start: 1. Enter the url: 2. Set karyotype information (see #Options->1 below). 3. Add your VCF data files (see #Options->3, #Input Formats->1 below). Additionally, for annotation purposes, the user can choose to plot the names of annotated genes, next to their genomic locations. Gene annotations are automatically fetched from the UCSC genome browser, or uploaded by the user in case of non-model organism (see #Options->4, #Input Formats->3 below). 4. Generate your rings (see #Options->5 below). 5. Click on the green "play" button and confirm your data submission. 6. Type your A link to the resulted plot file will be sent to your (see #Options->6, #Output File below). Rings Types: Two options available for presenting SNP information: 1. SNPs density: In this option, each plotted line represents the number of SNPs found within a defined genomic range(genomic length in bp). The darker the color, the more dense is that region. This option is recommended when whole genome visualization is required Density Range (bp): The SNPs Density algorithm counts SNPs in each range, after filtering the data by using the condition tree (see #Options->5.3 below). When creating or editing a ring, the user should set the desired range (genomic length) SNPs density will be calculated per this range (see #Options- >5.1, #Options->5.2 below). 2. Equalization to reference: In this option, a line is drawn at a corresponding SNP location. The line which represents a single SNP can be colored based on the genotype. Homozygosity to the reference allele will be colored yellow, homozygosity to the alternative red and heterozygosity blue. This representation option is recommended when plotting relatively small number of SNPs, or a single chromosome variations Column for preview (from uploaded VCF file): The Equalization to Reference algorithm allows the user to preview only one genomic column per ring.

2 When creating or editing a ring, the user should select a column for preview (see #Options->5.1, #Options->5.2 below). For example, if there are two columns A,B ( two samples in the VCF file), and the user would like to plot all SNPs having different genotypes when comparing A to B, the user after setting a condition tree, has to choose which sample to plot, A or B. Condition Tree: (see #Options->5.3 below) The conditions tree allows you to filter the ring data by whole genome comparisons with complex conditions. All positions that will meet the defined conditions will be presented in the specified ring according to the chosen ring type (see #Rings Types above). Input Formats: All input files should be tab-delimited. 1. Genomic data file- The file should be in VCF4.2 format and have a header line starting with #. The total size of the uploaded files should not reach 1Gb. 2. Karyotype file- has two columns, chr and chr length (bp). The allowed maximum file size is 5Mb. 3. Annotation file- has 4 columns: chr, start, end, annotation (gene name for example). The allowed maximum file size is 10Mb. Output File: The output is a SVG file created based on your VCF data files and your preferences. A link to the resulted plot file will be sent to your . Options: 1. Update Karyotype information: 1.1. Click on "Data" button in the right menu Click on "Karyotype" button The user has three options: Load from UCSC- choose your species of interest and its database building version from the drop-down menu, and its karyotype will automatically be fetched from UCSC Load from file- click on "LOADFROM FILE" button and select your karyotype file (see #Input Formats->2 below) Create your own karyotype- click on "ADD NEW CHROMOSOME" button and set the karyotype information. * Please note that CircosVCF will draw only the chromosomes that are found in the karyotype, therefore the chromosomes names in the karyotype file must identical to the chromosomes names in the VCF data files! 1.4. Click on "SAVE" button. 2. Data Files: 2.1. Add new VCF file: Click on "Data" button in the right menu.

3 Click on "+" button Select your VCF data files (see #Input Formats->1 above) Remove file from files list: Click on "Data" button in the right menu Right click on file button Click on "Remove" button. 3. Annotations: 3.1. Add/update annotations: Click on "Data" button Click on "Annotations" button Select an option: Load karyotype from UCSC: Select "LOAD FROM UCSC" Select the species and build Click on "SAVE" button Load karyotype from file: Select "LOAD FROM FILE" Select a file (see Input Formats->3 above) Click on "SAVE" button Remove annotations: Click on "Data" button Click on "Annotations" button Select "DON`T SHOW ANNOTATIONS" Click on "SAVE" button. 4. Rings: 4.1. Add new ring: Click on "RINGS" button in the right menu Click on "+" button Type ring information: Ring name to be displayed only in the rings list Percentage ring size of the external ring diameter Ring type (see #Rings Types above) Create a ring s condition tree (see #Options->5.3 below) Type a density range or select a column for preview (see #Rings Types- >1.1, #Rings Types->2.1 above) Click on "SAVE" button Edit ring: Click on "RINGS" button in the right menu Right click on ring button Click on "Edit" button Edit your ring information and conditions tree (see #Options->5.1.3, #Options->5.3) Click on "SAVE" button Space between rings: Click on "RINGS" button in the right menu.

4 Click on "Space Between Rings" button Set a percentage space between rings, calculated from the external ring diameter Click on "SAVE" button Ring s Condition tree: (see #Ring s Condition Trees above. Used in #Options- >5.1.4 and #Options->5.2.4) Add a new condition: Click on "+" button Add a condition Click on "SAVE" button. * Please note that the new condition will always be added to the right position of the condition tree, except when clicking on "+" button of the root, then the new condition will be added to the left position of the tree. Please see a detailed example at the end of this documentation Edit a condition: Right click on a condition Edit the condition Click on "SAVE" button Copy ring: Click on "RINGS" button on the right menu Right click on ring button Click on "Copy" button Delete ring: Click on "RINGS" button in the right menu Right click on ring button Click on "Delete" button Change rings ordering: Click on "RINGS" button in the right menu Long press on ring button Move mouse up or down to change ring position. 5. Finish and Run: 5.1. Click on the green "play" button at the lower part of the right menu Confirm your data Click on "SUBMIT" button Enter and confirm your Click on "NEXT" button At the end of the process a link for the resulted plot file will be sent to your . Do not close your browser until files upload will be completed (see #Output File above).

5 Example of ring s condition tree: a. Starting mode. For adding a new AND condition, click on "+" button, then select "AND tree" in the drop-down menu, and finally click on the "SAVE" button. This will be resulted with a new sub tree, which all its branches will be connected by an AND condition. b. For adding a new sub-condition of "equal columns" to the "AND tree", click on the right "+" button, then select "Equal columns" in the drop-down menu, next click on a,b,c buttons to select them, and finally click on the "SAVE" button. The AND condition has a new subcondition of a=b=c. c. For adding a new "Inequal columns" subcondition to the "AND tree", click on the right "+" button, then select "Inequal columns" in the drop-down menu, next click on i,h buttons to select them, and finally click on "SAVE" button. The AND condition has a new subcondition of i!=h. d. The final condition tree visualization

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