What does MAF mean in UNCLASSIFIED
Mutation Annotation Format (MAF) is a text-based file format commonly used in genomics to store information about genetic variants or mutations. The MAF format is designed to be used for the interchange of data between variant calling pipelines, annotation tools, and other bioinformatics programs. The key benefit of this standardized format is that it allows different pipeline components to easily communicate and exchange data with one another.
MAF meaning in Unclassified in Miscellaneous
MAF mostly used in an acronym Unclassified in Category Miscellaneous that means Mutation Annotation Format
Shorthand: MAF,
Full Form: Mutation Annotation Format
For more information of "Mutation Annotation Format", see the section below.
Definition
The MAF format stores information on genetic variants including single nucleotide polymorphisms (SNPs), insertions/deletions (indels), copy number variations (CNVs), and structural variations (SVs). It consists of lines of tab-separated values which start with a header line listing the columns followed by lines containing data for each variant. Each column holds information on specific aspects of the mutation such as chromosome, position, reference allele, alternate allele, consequence type, gene name and many others.
Use Case
MAF can be used in a variety of ways. It may be used when performing variant calling across an entire genome or when analyzing isolated genes or regions. Through its standardization, different pipelines can share results more easily than if using custom tabular formats or VCFs. This is especially beneficial in scenarios where multiple components must interact in order to perform efficient analysis; for example when a variant caller produces an initial set of candidates that are then passed to an annotation tool before being filtered and presented to a clinician.
Essential Questions and Answers on Mutation Annotation Format in "MISCELLANEOUS»UNFILED"
What is Mutation Annotation Format (MAF)?
MAF is a data exchange format that allows scientists to store, transmit and analyze information on genetic mutations made accessible by sequencing projects. The format is an eXtensible Markup Language (XML) based tab-delimited text file, which can be read by many different software programs and other applications. MAF files come in two flavors: somatic, which contains tumor specific mutations; and germline, which contains information about alleles present in normal individuals.
How many types of files types does the MAF use?
The MAF uses two types of file formats; somatic and germline files. Somatic files contain tumor specific mutations while germline files contain alleles present in normal individuals.
How do I create a MAF file?
To create a MAF file, you will need to prepare your data according to the guidelines published in the official GDC Technical Documentation. You must also include valid headers for all fields defined in the official GDC Data Dictionary, ensuring that no additional columns are inserted in the table. Once these steps have been completed, you can then generate your MAF file using any appropriate software tools or scripts.
Can I view my data in an interactive graphical representation with a MAF file?
Yes! With a valid DNAnexus account you can view your data within an interactive visual interface via the DNAnexus Platform App VCF Viewer by loading the corresponding variants from either a somatic or germline formatted MAF file.
Is there software available to help me with my analysis?
There are several user-friendly open source platforms available to assist with performing efficient analysis on mutation annotation format (MAF) files. These platforms include but are not limited to Oncotator Suite, MuTect2, VarScan2 and Somatic Sniper. Additionally there are many proprietary software options such as FireBrowse and CureFFI developed specifically for working with large scale datasets encoded as variant call format (VCF) or mutation annotation format (MAF).
What type of information can be found in a somatic formatted MAF File?
A somatic formatted MAFFile will generally provide information regarding single nucleotide variants (SNVs), insertion deletions (INDELs), gene fusions/translocations and non-coding regulatory elements associated with cancer cells obtained through sequencing projects such as next-generation sequencing (NGS). Additional pertinent data points located within this type of MAFFile include allele frequency observed across multiple samples, reference/alternative alleles or genotype call of mutated sequence and overall impact on downstream pathways/gene expression levels due to alteration observed at target site(s).
Final Words:
In summary, MAF provides a standardized way of exchanging data related to genetic variants between various tools and pipelines in bioinformatics applications. By allowing these components to communicate without loss of information while reducing potential incompatibilities due to custom formats, the MAF format greatly increases the efficiency at which genomic research can be performed.
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