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WGLab / InterVar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
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ANNOVAR #73

Open Nanditha-shetty opened 2 years ago

Nanditha-shetty commented 2 years ago

perl table_annovar.pl example/ex1.avinput humandb/ -buildver hg38 -out myanno -remove -protocol refGene,cytoBand,genomicSuperDups,esp6500siv2_all,1000g2012apr_all -operation g,r,r,f,f -nastring . -csvout

NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior) Error: the required database file humandb/hg38_ALL.sites.2012_04.txt does not exist.

I'm getting the required database file humandb/hg38_ALL.sites.2012_04.txt does not exist error.

I ran the below commands. for the table_annovar.pl command I'm getting the above error

PLEASE HELP!!!

perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene humandb/
perl annotate_variation.pl -buildver hg38 -downdb genomicSuperDups humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar snp138 humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar dbnsfp42a humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar esp6500siv2_all humandb/
perl table_annovar.pl example/ex1.avinput humandb/ -buildver hg38 -out myanno -remove -protocol refGene,cytoBand,genomicSuperDups,esp6500si_all,1000g2012apr_all -operation g,r,r,f,f,f,f -nastring . -csvout

quanliustc commented 2 years ago

do you try "1000g2015aug" for 1000 genome data?

kaichop commented 2 years ago

For genome build hg38, you have to use more recent 1000g versions.

Try

perl annotate_variation.pl -buildver hg38 -downdb 1000g2015aug humandb/

To download the latest 1000g data, and then proceed.

On Thu, Dec 23, 2021 at 5:36 AM Nanditha-shetty @.***> wrote:

perl table_annovar.pl example/ex1.avinput humandb/ -buildver hg38 -out myanno -remove -protocol refGene,cytoBand,genomicSuperDups,esp6500siv2_all,1000g2012apr_all -operation g,r,r,f,f -nastring . -csvout

NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior) Error: the required database file humandb/hg38_ALL.sites.2012_04.txt does not exist.

I'm getting the required database file humandb/hg38_ALL.sites.2012_04.txt does not exist error.

I ran the below commands. for the table_annovar.pl command I'm getting the above error

PLEASE HELP!!!

perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene humandb/ perl annotate_variation.pl -buildver hg38 -downdb genomicSuperDups humandb/ perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar snp138 humandb/ perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar dbnsfp42a humandb/ perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar esp6500siv2_all humandb/ perl table_annovar.pl example/ex1.avinput humandb/ -buildver hg38 -out myanno -remove -protocol refGene,cytoBand,genomicSuperDups,esp6500si_all,1000g2012apr_all -operation g,r,r,f,f,f,f -nastring . -csvout

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Nanditha-shetty commented 2 years ago

Thank you. This helped me a lot