depending on your command line, if you use this 1000g file, then you need

Question

depending on your command line, if you use this 1000g file, then you need

Nanditha-shetty opened this issue 3 years ago · 3 comments

depending on your command line, if you use this 1000g file, then you need
to install ANNOVAR and then download this file from ANNOVAR.

On Fri, Dec 24, 2021 at 1:23 AM Nanditha-shetty @.***>
wrote:

Error : The required database file humandb/hg38_ALL.sites.2012_04.txt
doesn’t exist.

Im getting the above error in annovar.
Do i need to download any database to continue further.

Anyone PLEASE HELP!!!!

—
Reply to this email directly, view it on GitHub
#75, or unsubscribe
https://github.com/notifications/unsubscribe-auth/ABNG3OBE2LBJKLQSDVFBEILUSQGVTANCNFSM5KWDLHVA
.
You are receiving this because you are subscribed to this thread.Message
ID: @.***>

Originally posted by @kaichop in #75 (comment)

Answer 1 · 2021-12-29T13:53:12.000Z

Iam getting only the intergenic region in my annovar ouptput file.
What is the reason for this?
I need to identify the missense variants. Is that any modification needed in the commands for this issue

Im newly using annovar tool. Please help

Answer 2 · 2021-12-29T14:41:21.000Z

If your input variants are intergenic variants, then output will be intergenic as well. You probably want to use ANNOVAR to annotate mutations first, making sure that the correct genome coordinate is used, before using intervar.

…

On Wed, Dec 29, 2021 at 8:53 AM Nanditha-shetty ***@***.***> wrote: Iam getting only the intergenic region in my annovar ouptput file. What is the reason for this? I need to identify the missense variants. Is that any modification needed in the commands for this issue Im newly using annovar tool. Please help — Reply to this email directly, view it on GitHub <#76 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3ODJNEIE7MQRJ2RY3ZDUTMHFHANCNFSM5K57W5QQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

Answer 3 · 2021-12-31T17:40:28.000Z

I have used the below commands.

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 dbnsfp42a humandb/

perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar esp6500siv2_all humandb/

perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar avsnp150 humandb/

perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar 1000g2015aug_all humandb/

perl table_annovar.pl new.avinput humandb/ -buildver hg38 -out myanno -remove -protocol refGene,cytoBand,dbnsfp30a,genomicSuperDups,esp6500siv2_all,1000g2015aug_all -operation g,r,f,r,f,f -nastring . -csvout -polish -xreffile example/gene_fullxref.txt