Supported File Types
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.
GFF3/GFF Format
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.
BED Format
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.
SAM/BAM Format
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.