GAP(GTF Annotation Parser) is a tool written in Python 2.7 for parsing Gencode/Ensembl GTF files and NCBI GFF3 annotation files. Input a GTF/GFF3 file, it will produce a *.genomeCoor.bed and a *.transCoor.bed file. Users can get transcript information by use a *.genomeCoor.bed file and module.

Download GAP 1.0.0 Manual First version
Download GAP 1.0.1 Manual Fix a serious NCBI gene type error
Download GAP 1.1.0 Manual Support Coordination Convert(Gene/Genome/Transcript)
Download GAP 1.1.1 1. Fix unsorted UTR string issue; 2. Support current NCBI GFF3 format

New!! GAP has been migrated to


Annotation Source UTR/CDS length distribution UTR/CDS median length
Gencode GRCh38 GTF UTR5: 189
UTR3: 463
CDS: 804
NCBI GRCh38.p7 GFF3 UTR5: 251
UTR3: 981
CDS: 1590
Gencode GRCm38 GTF UTR5: 169
UTR3: 547
CDS: 942
NCBI GRCm38.p4 GFF3 UTR5: 234
UTR3: 869
CDS: 1545

Contact Li Pan if you have any questions about this tool.