Annovar

Question

[1si17bt025]

What is the reason that i am getting only the intergenic regions in my annovar ouptput file.

I want to identify the missense mutations.

Please help!!

Thanks

[Zeng Jingyu]

I guess you have to post more information, like your code and the databases you used to annotate your files.

And I guess this time you didn't use the proper data. Please post your code here.

[Nanditha]

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