Which version of 1000G database is used for wANNOVAR? about doc-annovar

[kaichop]

There are multiple versions as described in https://annovar.openbioinformatics.org/en/latest/user-guide/download/ Please show the actual command. Did you actually download the data sets before running table_annovar? Also you need to specify the subpopulation such as 1000g2012apr_asn, instead of 1000g2012apr only.

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On Sat, Mar 25, 2023 at 6:44 PM Weiyan Jia ***@***.***> wrote: Thank you very much for your excellent tool. I have two questions as follow: 1. Which version of the 1000G database is used for wANNOVAR? 2. Which 1000g database should I use for the local run? I tried downloading the "1000g2015aug (6 data sets)", running table_annovar.pl, and got an error: "Error: the required database file humandb/hg19_1000g2015aug.txt does not exist.". I do see multiple 1000g2015-related files in the downloaded database folder. How do you think I should deal with this issue? Thanks, Weiyan -- — Reply to this email directly, view it on GitHub <#218>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OD4SFXN2P4MAA2YS2LW55YMNANCNFSM6AAAAAAWHZGAIM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[biofisherman]

Thank you very much for your quick response!

I tested it out as you suggested.

I have to specify the exact names of the downloaded database files. For example, I must use ALL.sites.2014_10,EAS.sites.2014_10,... NOT the table name: 1000g2014aug.

Best,

Weiyan

[kaichop]

No, you cannot use ALL.sites.2014_10. FAQ #4 explains this problem.

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On Tue, Mar 28, 2023 at 11:27 AM Weiyan Jia ***@***.***> wrote: Thank you very much for your quick response! I tested it out as you suggested. I have to specify the exact names of the downloaded database files. For example, I must use ALL.sites.2014_10,EAS.sites.2014_10,... NOT the table name: 1000g2014aug. Best, Weiyan — Reply to this email directly, view it on GitHub <#218 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OG42MFZA4QLWKMWO23W6L7NBANCNFSM6AAAAAAWHZGAIM> . You are receiving this because you commented.Message ID: ***@***.***>

[biofisherman]

Thank you again for your correction!

I tested it, and it worked by running the following command: perl table_annovar.pl annovarInput.tsv humandb/ -buildver hg19 -out output 1000g2015 -remove -protocol ensGene,1000g2015aug_all,1000g2015aug_eur,1000g2015aug_afr,gnomad211_exome -operation g,f,f,f,f -nastring . -polish -otherinfo

I got the same results as used ALL.sites.2015_08.

[kaichop]

Yes. The old version of ANNOVAR does not support ALL.sites.2015_08 so there are many issues when users use this keyword, so the newer version automatically converts this keyword to the 1000g2015aug_all and so on.

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On Tue, Mar 28, 2023 at 1:55 PM Weiyan Jia ***@***.***> wrote: Thank you again for your correction! I tested it, and it worked by running the following command: perl table_annovar.pl annovarInput.tsv humandb/ -buildver hg19 -out output 1000g2015 -remove -protocol ensGene,1000g2015aug_all,1000g2015aug_eur,1000g2015aug_afr,gnomad211_exome -operation g,f,f,f,f -nastring . -polish -otherinfo I got the same results as used ALL.sites.2015_08. — Reply to this email directly, view it on GitHub <#218 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OBBBPIO6RN46BLEDSTW6MQZ5ANCNFSM6AAAAAAWHZGAIM> . You are receiving this because you commented.Message ID: ***@***.***>