error related to annovar software
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6 days ago
rheab1230 • 0

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.

rsid annovar VCF SNP • 168 views
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6 days ago
 -dbtype avsnp142

shouldn't it be

 -dbtype snp142

?

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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/ 
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Thank you I am able to do it

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