CrossMap

CrossMap is versatile tool to convert genome coordinates or annotation files between genome assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF, GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF and VCF, reading from remote servers and file compression are supported.

GFF / GTF

Your input data should be either GTF/GFF2.5 or GFF3 format.

GFF (General Feature Format) is another plain text file used to describe gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The first eight fields are the same as GFF. Only chromosome and genome coordinates are updated. The format of output is determined from the input.

Notes:

• Each feature (exon, intron, UTR, etc) is processed separately and independently, and we do NOT check if features originally belonging to the same gene were converted into the same gene.
• If user want to liftover gene annotation files, use BED12 format.