Annotation file formats

Question

[Pfs]

Besides GTF (GFF) and BED, are there other annotation file formats out there? Which one is predominant?

I use almost exclusively GTF, but I was wondering if there might be advantages in using other formats.

Thanks in advance.

[h.mon]

GTF and GFF are different file formats, even though GTF is sometimes called "GFF 2.5".

Answer 1

[Alex Reynolds]

BED, VCF, GFF/GTF/GVF, BAM/SAM, PSL (Blat), RepeatMasker, etc.

Answer 2

[james.lloyd]

In my experience GTF and GFF are the main two and are very similar to each other and the advantages might only relate to the 9th column but as they both use semi-colons to separate fields, they both cause me a problem when I found gene names with ; in it!