GATK - dbSNP .rod files

[Kath]

Hi,

I am using GATK to adjust my per base quality scores in a .bam file. Does anyone know how to download a dbSNP v132 .rod file in order to exclude already known variants so they are not interpreted as mismatches?

Also, can anyone recommend covariates to use in the CountCovariates analysis?

Thanks

Kath

[dawe]

You can build your own rod file (I've done this with hg19/db131): http://www.broadinstitute.org/gsa/wi.../The_DBSNP_rod

[Kath]

Thanks for your response. I had seen the website but found it assumed more informatics knowledge than I possess. For example, it tells you how to merge two rod files but not how to get the rod for dbSNP 132 in the first place...

[dawe]

Actually you don't need to have a rod file for dbsnp132:

http://getsatisfaction.com/gsa/topics/dbsnp132_rod

d

[Kath]

Thanks, I hadn't noticed that thread.
Kath