Question: VEP FASTA "toplevel" vs "primary_assembly"
gravatar for cocchi.e89
13 months ago by
cocchi.e8950 wrote:

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 ( 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 ( 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!

vep ensembl fasta • 599 views
ADD COMMENTlink written 13 months ago by cocchi.e8950

If you intend to use VEP then follow their recommendation.

ADD REPLYlink written 13 months ago by genomax83k
gravatar for WouterDeCoster
13 months ago by
WouterDeCoster43k wrote:

See this blog post:

ADD COMMENTlink written 13 months ago by WouterDeCoster43k
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