Difficult to understand documentation with regard to sqlite databases

[allaway]

I am trying to annotate some variants using the exac_03 database. I retrieved it using download.database(), but it retrieved the following database: hg19_exac03.sqlite.sql. It's now in my "annovar/humandb" directory.

When I try x <- annotation(dat = dat, anno.name = "exac03", database.dir = "annovar/humandb", db.type = "sqlite")
I get the following error:

Error in dbname.initial(anno.name, dbname.fixed, setdb.fun, buildver,  : 
  annovar/humandb/hg19_exac03.sqlite sqlite format database dose not exist.

Is there a step I am missing between retrieving the db and running annotation? Thanks!

[Miachol]

I'm sorry about this. The document of annovarR is incomplete now,

I guess you need to install the SQLite3 before installing the SQLite format exac03 database. If the sqlite or sqlite3 not in PATH, the converting step in download.database may not work.

# After installing SQLite3
annovarR::sql2sqlite('/path/hg19_exac03.sqlite.sql', dbname = '/path/hg19_exac03.sqlite')
# If you have downloaded the text format `hg19_exac03.txt`
sqlite.auto.build("exac03", buildver = hg19"", database.dir = "/path/humandb")`

In fact, you can also use the perl version ANNOVAR to do the exac03 annotation.

x <- annotation(dat = dat, anno.name = "perl_annovar_exac03", database.dir = "~/.annovarR/db", annovar.dir = "/opt/bin/annotation/annovar/20170716/")

[allaway]

Dear Jianfeng, Thank you for the help! That makes sense. I'll make sure sqlite3 is in my path. In the interim, I used the perl version on the command line, which worked well. In the future, I'll try to incorporate annovarR into my workflow. Cheers, Robert

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On Thu, Jun 28, 2018 at 7:32 PM Jianfeng ***@***.***> wrote: I'm sorry about this. The document of annovarR is incomplete now, I guess you need to install the SQLite3 <https://www.sqlite.org/index.html> before installing the SQLite format exac03 database. If the sqlite or sqlite3 not in PATH, the converting step in download.database may not work. # After installing SQLite3annovarR::sql2sqlite('/path/hg19_exac03.sqlite.sql', dbname = '/path/hg19_exac03.sqlite')# If you have downloaded the text format `hg19_exac03.txt` sqlite.auto.build("exac03", buildver = hg19"", database.dir = "/path/humandb")` In fact, you can also use the perl version ANNOVAR to do the exac03 annotation. x <- annotation(dat = dat, anno.name = "perl_annovar_exac03", database.dir = "~/.annovarR/db", annovar.dir = "/opt/bin/annotation/annovar/20170716/") — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ATdmyG_yeQ1q7AzpRB_3ASU6a9q5W7MPks5uBZG7gaJpZM4U74xf> .