annotation with annovar

[tahamasoodi]

Hi,

Is it possible to get a single output file after applying the annotations (1000 genome, dbSNP, SIFT etc) to a vcf file?

[yl01]

Yes, SUMMARIZE_ANNOVAR can just do it. See it on the annovar home page.

[tahamasoodi]

I used SUMMARIZE_ANNOVAR but it is giving output in seperate files (for 1000 genome, dbSNP 135, SIFT etc). I want a single output file containing all these annotations.

[tahamasoodi]

Can anybody tell me what is the exact command to get a single output excel file using annovar?
Another question, will annovar work for whole genome sequences?

[tahamasoodi]

I did not get any further responses for my query. Is anybody who can help?

[mamons]

summarize_annovar.pl outputs a excel file with annotated variants after filtering using the pipeline explained here:

http://www.openbioinformatics.org/annovar/annovar_accessary.html

If you want to keep the variants from the different filter steps, or do the filtering your own way, you have to collect the variants yourself.

[arcolombo698]

no for the single output use table_annovar.pl