How to find out the reference info from every snp or indel from result of annovar?

[hellsingwyk]

HI all~

Did anyone use annovar for annotation before?
It is a very powerful annotation tool using .vcf file as input. However, I am not sure how could I obtain the reference information for each snp or indel.

Could anyone give me a hand?

Best Regards,
Michael

[HESmith]

The output of ANNOVAR includes both the reference and variant alleles in the columns after the chromosome and position.

[hellsingwyk]

Thank you very much!!!