Changing strand orientation in VCF files

[sagi.polani]

Hi everyone,

I'm looking for a way to change the strand orientation in a VCF file. Specifically, I'm looking to change the strand orientation of a dbSNP VCF file so that all variants will be in the + strand orientation (genome orientation) and NOT according to refSNP (transcript orientation).

I'd appreciate any help on this matter.

Thanks!

Sagi

[dpryan]

You could do this in any programming language, directly with awk/sed/etc, or even Excel.

[sagi.polani]

Hi,

I'm not really a big script writer - any specfic recommendations on which commands to use?

Thanks,

Sagi