ANNOVAR

[Nanditha-shetty]

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]

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

[kaichop]

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 — Reply to this email directly, view it on GitHub <#73>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OB547HXTKWBO2SPTG3USL3STANCNFSM5KUPRKXQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Nanditha-shetty]

Thank you. This helped me a lot