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Old 01-15-2015, 10:26 PM   #1
hellsingwyk
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Default How to find out the reference info from every snp or indel from result of annovar?

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
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Old 01-16-2015, 04:31 AM   #2
HESmith
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The output of ANNOVAR includes both the reference and variant alleles in the columns after the chromosome and position.

Last edited by HESmith; 01-16-2015 at 04:31 AM. Reason: more detail
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Old 01-20-2015, 03:28 PM   #3
hellsingwyk
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Thank you very much!!!
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