Question: Annovar Annotation With 1000G
1
gravatar for daphnarisseeuw
5.9 years ago by
daphnarisseeuw20 wrote:

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?

annovar 1000genomes • 4.0k views
ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by daphnarisseeuw20

did you try to open

annotate_variation.pl script in line 1962 and see what is written in it?

as shown in the error in your question it expecting some thing to check against "numeric" but instead it find & give it a try and see annotate_variation.pl at 1962 or around it.

ADD REPLYlink modified 5.9 years ago by Istvan Albert ♦♦ 78k • written 5.9 years ago by Medhat8.0k

I encounter the same issue as yours. But I still don't know how to solve this.

ADD REPLYlink written 27 days ago by George.Robert0
3
gravatar for Jorge Amigo
5.9 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

you are getting this error because annotate_variation.pl seems to be filling $end with the reference allele column (line 1962 contains an equivalence check for $start and $end), but you only would have entered in that "else" section if the line you are processing isn't recognized as a 1000g data line. since the software you're using is the same as the one we others use (unless you have edited it, of course), the only thing I can think of is that you're using wrong 1000g data files.

make sure you download the 1000g data files as follows:

perl annotate_variation.pl -downdb -buildver hg19 1000g2012feb humandb

and then you filter/annotate your data like this:

perl annotate_variation.pl -filter -dbtype 1000g2012feb_all -buildver hg19 testfile1.txt humandb

of course, you may change the above "1000g2012feb" tag for any desired 1000g version available.

ADD COMMENTlink written 5.9 years ago by Jorge Amigo11k
2

in case you are using hg18 you should go for the appropriate databases. in the subsection number 4 of the "Prepare Database" section you'll see a list of databases and their corresponding reference: some will have both hg18 and hg19 options, some will be only available for one reference only. just download the ones you are interested in and the ones that suit your experiment's requirements. a detailed list of the available databases to download can be found here.

moderator's note: if you need to comment or ask anything just press the appropriate button down here, avoiding creating answers with new questions. if you need to modify your initial question you can edit it, and if you need to ask something new just post a new one.

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Jorge Amigo11k

Excuse me:

i encountered another question when i use annovar.The commmand was as follows:perl convert2annovar.pl -format vcf4 input.vcf -outfile output.avinput -allsample -withfreq -include -withzyg

Then is printed the error message "Use of uninitialized value $zygosity in join or string at /home/linan/annovar/convert2annovar.pl line 2112, <VAR> line 143.
Can't use an undefined value as a symbol reference at /home/linan/annovar/convert2annovar.pl line 2112, <VAR> line 143."

i do not know why.thx in advance.

Hoping for your reply!

ADD REPLYlink written 4.2 years ago by 89759864480

you should open a new question, instead of commenting a (rather old) previous answer. before you create it, have in mind that maybe the "-include" option you are using should be the "-includeinfo", and that the -withfreq and -withzyg options used together generate pairs of annotations, one with frequency and other with zygosity information. you may want to further study your command before asking for help.

ADD REPLYlink written 4.2 years ago by Jorge Amigo11k
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