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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Downloads for ensGene, ensGene40 for hg38 no longer work #210

Closed slagelwa closed 1 year ago

slagelwa commented 1 year ago

Looks as if UCSC is no longer providing the file:

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ensGene.txt.gz

which means that the commands:

annotate_variation.pl --buildver hg38 --downdb ensGene /tmp
annotate_variation.pl --buildver hg38 --downdb ensGene40 /tmp

no longer work.

slagelwa commented 1 year ago

Didn't see this in the FAQ:

Switching to hg38 Ensembl gene annotation Note that ensGene for the hg38 is not made available by UCSC Genome Browser. A user pointed out that UCSC have replaced the ensGene.txt using GENCODE starting from version 22...

So its covered there.