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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Argument "T" isn't numeric in **exac03** file #206

Open xiucz opened 1 year ago

xiucz commented 1 year ago

Hi , I knew the bug here in 1000G dataset, but how to solve this problem in exac03 database? Here is my command,

annovar-2020-06-07/table_annovar.pl \
--vcfinput decomposed.vcf \
--outfile decomposed --buildver hg19 ~/hg19/humandb \
--otherinfo --remove --protocol exac03 --operation f --polish  --thread 6

Best, xiucz

kaichop commented 1 year ago

The command looks correct to me. Try remove thread argument and see if it works. Also use tail command to check the last line of the exac03 file in case your file downloaded is corrupted. Also it is helpful to print out the full LOG information after running the command. There is no bug in 1000G dataset. Some users did not know the argument to use for 1000G data because of the historical reasons that the argument is different from file name.

On Thursday, December 22, 2022, xiucz @.***> wrote:

Hi , I knew the bug here in 1000G dataset, but how to solve this problem in exac03 database? Here is my command,

annovar-2020-06-07/table_annovar.pl \ --vcfinput decomposed.vcf \ --outfile decomposed --buildver hg19 ~/hg19/humandb \ --otherinfo --remove --protocol exac03 --operation f --polish --thread 6

Best, xiucz

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/206, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OEVCL4OIX4WJ4IYKXTWOQFMJANCNFSM6AAAAAATGOLIKM . You are receiving this because you are subscribed to this thread.Message ID: @.***>

xiucz commented 1 year ago

Thank you! After re-downloading the exac03 file, there are no warnings anymore, I think the old file I downloaded is corrupted. And I will close the issue.