What is genotype quality score?

What is genotype quality score?

The Genotype Quality represents the Phred-scaled confidence that the genotype assignment (GT) is correct, derived from the genotype PLs. Specifically, the GQ is the difference between the PL of the second most likely genotype, and the PL of the most likely genotype.

What is a VCF file and how do I open it?

How to Open a VCF File. VCF files can be opened by a program that lets you view the contact details but the most common reason to open such a file is to import the address book into an email program, like one online or on your phone or computer.

What is genotype likelihood?

Genotype likelihoods are in this context the likelihood the data given a genotype. This is to be understood as we take all the information from our data for a specific position for a single individual, and we use this information to calculate the likelihood for our different genotypes.

How do I create a VCF file?

Save a contact as a vCard

1. In the open contact, click the Microsoft Office Button. , point to Save As, and then click Export to vCard File.
2. Type a name in the File name box, and then click Save.

How do I convert a VCF file?

How to convert . VCF files to . CSV for email contacts

1. In Windows File Explorer, navigate to your Contacts folder (for example, C:\Users\UserName\Contacts).
2. Navigate to the VCF contacts file you wish to import.
3. Enter a name for your exported file and use the Browse button to find a location in which to save the file.

What is the purpose of a VCF file?

Variant Call Format (VCF) is a format for storing and reporting genomic sequence variations. VCF files are modular where the annotations and genotype information for a variant are separated from the call itself.

Where can I find the VCF format spec?

The VCF specification used to be maintained by the 1000 Genomes Project, but its management and further development has been taken over by the Genomic Data Toolkit team of the Global Alliance for Genomics and Health. The full format spec can be found in the Samtools/Hts-specs repository, along with other useful specifications like SAM/BAM/CRAM.

Which is the special kind of VCF called gVCF?

For information on the special kind of VCF called GVCF produced by HaplotypeCaller in -ERC GVCF mode, please see the GVCF entry. For information specific to SOMATIC calls, see the Mutect2 documentation under the Tool Index. 1. Overview

How are filters defined in TCGA VCF 1.1v2-gdc?

FILTER fields are defined to list filtering criteria used for generating variant calls. Custom filters can be applied as long as a definition is provided in the HEADER. FILTERs that have been applied to the data should be described as follows. Please note that FILTER declarations do not include Type or Number keys.