Download vcf file sample

While majority of the steps pertaining to the basic structure of the file remain the same, checks for supplemental information fields have been introduced.

The first column, "Customization type", indicates whether a new validation step has been introduced or if an existing step has been modified. The following example based on VCF version 4. Any VCF file contains two main sections. Both sections are described below. Case-sensitivity : Please note that all fields and their associated validation rules are case-sensitive as given in the specification unless noted otherwise.

Meta-information could be applicable either to all variant records in the file e. The following table lists some of the reserved field names. Files can be customized to contain additional meta-information fields as long as they are not in conflict with reserved field names.

The first field in Table 2 fileformat is mandatory and lists the VCF version number of the file. Different keys that can be used to define them are described in Table 3. All three fields do not use the same set of keys. Please refer to individual field definitions for further details. Please refer to Tables 4 and 5 for details. If a sub-field exists in these tables and is used in a TCGA VCF file, then all pairs in the definition should match entries in the corresponding table for the file to pass validation.

INFO fields are optional and contain additional annotations for a variant. Custom INFO fields can be added based on study requirements as long as they do not use the reserved field names.

If an INFO field is declared in the header, it needs to be described further using the following format:. FORMAT declaration lines are used when annotations need to be added for individual genotypes associated with each sample in the file. Please refer to Table 5 for definitions for these sub-fields. SS can be 0, 1, 2, 3, 4, or 5 depending on whether relative to normal the variant is wildtype, germline, somatic, LOH, post-transcriptional modification, or unknown respectively. These should be considered as required fields so that they are included by default unless there is an exceptional scenario where the information for a field cannot be obtained.

In such a case, ". To ensure that all TCGA VCF files have consistent definitions for standard fields and to avoid merging errors due to contradicting definitions, following header declarations for common fields are proposed. By adhering to these definitions, we can ensure that a given field is interpreted the same way across all centers and that same 'Number', 'Type' and 'Description' values are used for these IDs.

In the case of tumor clonal populations, one population is clonally derived from another. Each of these samples should have its own HEADER declaration where the sample identifier in the column header should be the same as the value assigned to "ID" key in the corresponding declaration. The declaration lists information about the sample source, platform, source file, etc.

Format : Tab-delimited line starting with " " and containing headers for all columns in the BODY as shown below. This is a mandatory header line where the first 8 fields are fixed and have to defined in the column header. Data lines are tab-delimited and list information about individual variants and associated genotypes across samples.

The first 8 fields Figure 1 are required to be listed in the VCF column header line. Some of these fields require non-null values see Table 6 for each record. For the remaining fixed fields, even if the field does not have an associated value, it still needs to be specified with a missing value identifier ". Subsequent fields are optional. A variant representation format for cancer data should be able to support more complex variation types such as structural variants, complex rearrangements and RNA-Seq variants.

The following sub-sections present an overview of the extensions that have been added to clearly describe such variations in a VCF file. A structural variant SV can be defined as a region of DNA that includes a variation in the structure of the chromosome.

Such variations could be due to inversions and balanced translocations or genomic imbalances insertions and deletions , also referred to as copy number variants CNVs. If the GT subfield is present, it must be the first subfield. In the example, all genotypes are unphased, and the genotypes for SAMP are homozygote reference, heterozygote, and missing in the first, second, and third records. The second record contains a GP genotype probability format subfield, and the third record contains PL phred-scaled genotype likelihood format subfield.

It is not necessary for the genotype likelihoods to sum to 1. Released: July 20, Added: July 20, Visits: Released: July 06, Added: July 06, Visits: Released: May 03, Added: July 06, Visits: Windows Software. BeOS Software. Macintosh Software. Linux Software. PDA Software. Mobile Software.

Sample Press Release. Sample Event Press Release. Sample Press Release Format. Radio Music Script Sample. Sample Release Agreement. Broadcasting Script Sample. Employee Sample Data Contact Xls. Sample Phone Directory. Church Directory Sample. Free Sample Sales Promotion Letter.

Download : vCard Magic Download. Download : vCard Converter Download. Download 38 : vCard to Outlook Conversion Download. Download 34 : Import vCard Download. Download 34 : Batch vCard Import Download. Download 45 : Import vCard to Excel Download. Download 37 : Convert vCard to Excel Download. Download 41 : vCard to Excel Download. This displays the contact information prominently as an Electronic Business Card. For more information, see Include an Electronic Business Card in your e-mail signature.

To learn about creating. Attach a vCard to an email message Click New Email. Here's an example of what a vCard might look like. Save a contact as a vCard Saving contacts as vCards provides a way to efficiently store a large number of contacts.

Type a name in the File name box, and then click Save. To view a vCard or business card: In Contacts , select the Home tab. Top of page. Attach a vCard to an email message In Contacts , do one of the following: In any card view, drag the contact card and drop it into the body of an open message. A new message opens with the vCard attachment on the Attach line.

Complete the message and send.