why I miss genes in the annotations?

Question

[cristina_sabiers]

Hi!

Hope someone can clarify me this

I downloaded the gtf annotation from

http://www.gencodegenes.org/releases/26lift37.html

I generated my own bed file for annotate just the gen name on my vcf file, the fact is that I miss a few genes for example this one that don't appear (it does with annovar annotation), i also miss genes if I download from http://genome.ucsc.edu

chr1    158368309   T   G   1678.36 0   PASS    snp 0.000160388 [{'transcript':'NM_001004475.1','gene':'OR10T2','location':'downstream'}]

Does this happens to someone else?

Thanks

[theobroma22]

It could be differences in the release or version you are using. If it's an old or new version you should expect there to be differences since updates were made, and possibly to your gene as well. This is quite common.