Question: VEP FASTA "toplevel" vs "primary_assembly"
gravatar for cocchi.e89
4 weeks ago by
cocchi.e8920 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 • 142 views
ADD COMMENTlink written 4 weeks ago by cocchi.e8920

If you intend to use VEP then follow their recommendation.

ADD REPLYlink written 4 weeks ago by genomax67k
gravatar for WouterDeCoster
4 weeks ago by
WouterDeCoster39k wrote:

See this blog post:

ADD COMMENTlink written 4 weeks ago by WouterDeCoster39k
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