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Old 01-03-2012, 05:57 AM   #1
kjaja
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Default quation on using auto_annovar.pl

Hi,

I have a question related to auto_annovar.pl, why do we need to specify the mode of inheritance as dominant or recessive? I am not sure how this information is being used when doing the filtering. Can some give an example or explain it some more ? sorry of this is a trivial question but this is my first time working with this type of data.

In my case, I have variants called for 4 cases and want to indentify the variants that are in cases but not present in dbSNP or 1000 genome to identify the variants that are most likely to be deleterious. So I merged all the variants from the 4 cases in one vcf file (using VCFtools) and want to apply the auto_annovar.pl filtering on the set of the merged variants. Is there a better way to look at this?

Thanks for your help,
Kay

Last edited by kjaja; 01-03-2012 at 06:00 AM.
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