VEP FASTA "toplevel" vs "primary_assembly"

Question

[cocchi.e89]

Dear all, I am new to VEP, I am trying to use GRCh37 assembly with offline method and I need a FASTA file, I saw in their download section (https://useast.ensembl.org/info/data/ftp/index.html) that there are several options. The GRCh38 that the installer download in my folder is: Homo_sapiens.GRCh38.dna.toplevel.fa.gz so I downloaded the respective Homo_sapiens.GRCh37.dna.toplevel.fa.gz file, but I saw in their webpage (https://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta) that they advise to use the "primary_assempbly" (Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz).

What is exactly the difference between them and what shall I use?

Thanks a lot in advance for any help!

[GenoMax]

If you intend to use VEP then follow their recommendation.

Answer 1

[WouterDeCoster]

See this blog post: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use