Annovar -- annotation without filter?

[Robby]

Hello everyone,

I would like to annotate my SNPs. After annotation I would like to have a table with additional information like position (exon, intron, UTR,...), dbSNP-ID, SIFT/PolyPhen/PhyloP-score, gene (for exonic SNPs),....

I tried to use Annovar for that. But unfortunally I received two tables after each step and I couldn't use these tables for the next step, so that it wasn't possible to have for example the position/region together with the SIFT-score in one table or i.e. the Sift- and Polyphen-score in one table.

Is there any possiblity to add just the information to the table and use the resulting table for the next step?

Thanks for your help

[Jorge Amigo]

although rudimentary, you could use the summarize_annovar.pl script which is included in the ANNOVAR's distribution in order to have several annotations in the same table. since it loads several annotations tables into the memory you'll need a few GBs of RAM available on your computer (for hg18 annotation I remember I needed ~5GB). it is not very customizable, but it can maybe suit your needs as it did with ours. you can read a little more about the script on the ANNOVAR's Accessory Programs section.

[Robby]

thanks. that helps me a lot.

But I have some new questions:
I would like to use the new 1000G data (May 2011), but the script just accepts the old one (Nov 2010). Is there any possibility to change that?

Does anyone know, how annovar handels SNPs/Indels belonging to different isoforms/genes? Can I find just the result of one isoform in that case or are there different lines for each hit?

[Jorge Amigo]

for the first question (using 1000g2011may data instead of 1000g2010nov) I would suggest to do what we did and worked: edit the summarize_annovar.pl script and change all "1000g2010nov" occurrences for "1000g2011may".

for the second question I must also require help, since I believe that each SNP belonging to different isoforms is written on a separate line, but I haven't investigated it yet.