error related to annovar software

Question

[rheab1230]

Hello everyone, I am trying to use annovar software to update my .vcf files with rsdi of dbSNP. I am getting some error. the code is:

annotate_variation.pl -downdb -buildver hg19 avsnp142 humandb/
annotate_variation.pl ex1.avinput humandb/ -filter -build hg19 -dbtype avsnp142
the error: NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done
NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/avsnp142.txt.gz ... Failed
WARNING: Some files cannot be downloaded, including http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/avsnp142.txt.gz

Can anyone please help me out with this? Or does anyone know how to update id in .vcf files with rsid of dbSNP? Thank You.

Answer 1

[Pierre Lindenbaum]

 -dbtype avsnp142

shouldn't it be

 -dbtype snp142

?

[igor]

The avsnp142 part should be okay, but you may need to add -webfrom annovar. Check the available examples:

[kaiwang@biocluster ~/]$ annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avsnp147 humandb/ 

[rheab1230]

Thank you I am able to do it