Annovar annotation with 1000g

[Jamica]

Hello everyone,

I have recently downloaded Annovar, and succesfully filtered my files with a few databases, downloaded from Annovar.
But when I try to do the exact same thing with the 1000 genomes project database, I get this error many times in the terminal, one for each line of **.

Argument "*" isn't numeric in numeric eq (==) at annotate_variation.pl line 1962, <DB> line **.
* can be A, C, G, or T.
** every line of the database

I have tried filtering with 1000g, 1000g2010 and 1000g2010jul databases, but all give these errors.

An example of the commands I use for filtering:
perl annotate_variation.pl --filter --dbtype CEU.sites.2010_07 testfile1.txt humandb/

Can anyone tell me if I'm doing something wrong, if this is known, and if I can do anything about it?

[arkanion]

Hello everyone,

I have recently downloaded Annovar, and succesfully filtered my files with a few databases, downloaded from Annovar.
But when I try to do the exact same thing with the 1000 genomes project database, I get this error many times in the terminal, one for each line of **.

Argument "*" isn't numeric in numeric eq (==) at annotate_variation.pl line 1962, <DB> line **.
* can be A, C, G, or T.
** every line of the database

I have tried filtering with 1000g, 1000g2010 and 1000g2010jul databases, but all give these errors.

An example of the commands I use for filtering:
perl annotate_variation.pl --filter --dbtype CEU.sites.2010_07 testfile1.txt humandb/

Can anyone tell me if I'm doing something wrong, if this is known, and if I can do anything about it?

Have you fixed your problem? How?

I get the same error with the latest 1000g dataset, 1000g2015aug.zip which extracts 6 .txt files:

hg19_ALL.sites.2015_08.txt
hg19_AFR.sites.2015_08.txt
hg19_AMR.sites.2015_08.txt
hg19_EUR.sites.2015_08.txt
hg19_SAS.sites.2015_08.txt
hg19_EAS.sites.2015_08.txt

while running the command:

perl table_annovar.pl tumor-vs-normal.mutect.vcf humandb/ -outfile temp/myanno -protocol ALL.sites.2015_08 -operation f -nastring . -vcfinput -remove -thread 12

[HESmith]

Try using '-protocol 1000g2015aug_all' in your command, and let us know if that solves your problem or not.