VCMap provides support for loading custom user annotation from multiple file formats. For more information about loading custom annotation please visit our FAQ page or use the tutorial included in the VCMap application.
The GFF (General Feature Format) lines are based on the GFF standard file format. GFF lines have nine required fields that must be tab-separated. Undefined fields are replaced with the "." character. Unescaped quotation marks, backslashes and other ad-hoc escaping conventions that have been added to the GFF format are explicitly forbidden. The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.
The BED (Browser Extensible Data) format was designed at UCSC for displaying data tracks in the Genome Browser. BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The order of the optional fields is binding: lower-numbered fields must always be populated if higher-numbered fields are used.
The SAM (Sequence Alignment Map) format is a compact and index-able representation of nucleotide sequence alignments. The SAM format consists of one header section and one alignment section. The whole header section can be absent, but keeping the header is recommended. The BAM (Binary Sequence Alignment Map) format is the compressed binary version of the SAM format. For a more detailed description of the formats please download the format specification document.