Which version of 1000G database is used for wANNOVAR?

[biofisherman]

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

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[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.

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

--

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[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.

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

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[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.

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.

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