Question: Not able to filter 1000G (hg19_ALL.sites.2015_08.txt) in Annovar
1
gravatar for dsmarcoantonio
4.0 years ago by
Brazil
dsmarcoantonio40 wrote:

I am getting this error when using the 1000G to annotate may VCF:

Scanning filter database hg19_ALL.sites.2015_08.txt...Argument & isn't numeric in numeric eq (==) at annotate_variation.pl line 2277, <DB> line ###.

This error occurs in every line of the database.

On line 2277 from annotate_variation.pl seens that $start==$end because the hg19_ALL.sites.2015_08.txt only has start positions. But this database comes directly from annovar site.

Anyone know how to fix it??? What are I doing wrong???

 

I downloaded all databases using:

perl annotate_variation.pl -downdb -webfrom annovar --buildver hg19 1000g2015aug humandb

My commands are:

convert2annovar.pl -format vcf4 <vcf> -includeinfo -outfile <vcf_avinput> -allsample
table_annovar.pl <vcf_avinput> humandb -protocol refGene,phastConsElements46way,genomicSuperDups,exac03,esp6500siv2_all,esp6500siv2_ea,esp6500siv2_aa,ALL.sites.2014_10,snp137,snp138,avsift,clinvar_20150330,ljb26_all -operation g,r,r,f,f,f,f,f,f,f,f,f,f -buildver hg19 -otherinfo -remove -nastring . -outfile <annovar.vcf>

Thanks

forum • 2.3k views
ADD COMMENTlink modified 5 weeks ago by biotefarosero0 • written 4.0 years ago by dsmarcoantonio40

Hi, I have the same problem, how did you fix it?

ADD REPLYlink written 5 weeks ago by biotefarosero0

Hi biotefarosero,

please do not ask question in old threads, same here A: Annovar Annotation With 1000G. Please open a new question, provide the necessary background information.

ADD REPLYlink written 5 weeks ago by ATpoint23k
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